In Hesperides, when Gabriel Santiago tries to tell Orlando his theory that the Disciples came from Eligius III, Orlando interrupts him to tell Gabriel that the Shepherd delivered them to Bardo. Gabriel asks if the Shepherd had been on Eligius III as well, but Orlando refuses to answer the question, ordering Gabriel not to say his name. Gabriel later finds Orlando praying to the Shepherd and asks him if the Shepherd wouldn't understand their need to rescue their people. Gabriel brings up his own experience with people worshipping false gods and questions if the Shepherd would condone torturing Gabriel's friends who have done nothing to him or sending a man as devoted as Orlando to prison. Gabriel states that men condone those things and weak men follow their orders. Gabriel's argument successfully convinces Orlando to help them out.
On Sanctum, Captain Meredith gives Clarke Griffin a choice to come with the Disciples by choice or force, telling her that she is going to serve the Shepherd either way. However, the standoff is interrupted by Jordan Green and Raven Reyes who kill the Disciples using one of their own suits.
In Welcome to Bardo, Gabriel, Hope and Echo listen to a sermon by Anders in which he mentions the Shepherd delivering them to Bardo using the Anomaly Stone with one of the Disciples commenting that the native Bardoans went extinct because they didn't have the Shepherd to guide them. From Anders' sermon, Gabriel realizes that the Disciples weren't from Eligius III but were instead led to Bardo from Earth through the Anomaly itself.
In a flashback, while sending Captain Meredith on his mission, Anders tells the captain that the Shepherd is counting on him.
In The Queen's Gambit, Anders awakens Cadogan from his cryopod on Bardo. Cadogan is surprised to see Anders again and though Anders addresses Cadogan as the Shepherd, Cadogan tells Anders to just call him Bill. Cadogan realizes that if Anders awoke him so early he must have news and asks if they have cracked the code and if the war has begun. Anders admits that it hasn't yet, but they have the Key. Cadogan smiles, pleased by the news.
In Anaconda, Cadogan enters the Stone room unarmed and requests that Clarke's group let his people go. Cadogan tells the group that his followers call him the Shepherd but they can call him Bill. Clarke recognizes him as Bill Cadogan and explains to Niylah in Trigedasleng that his cult created the bunker and burned Becca Franko alive. Cadogan, understanding their conversation, is surprised, stating that they were not a cult but a conglomerate of some of the world's greatest minds. Cadogan states that his daughter created the language as a child and asks Clarke if Callie survives inside of the Key which Gabriel explains is the Flame.
In a flashback, Cadogan calls Callie to ask about her dropping out of MIT to join Tree Crew. The two argue about her choices when Cadogan suddenly gets news of a situation. At Cadogan's demand, Callie gets her mother Grace and Cadogan tells her "Anaconda." Cadogan reassures her that its real and she has 20 minutes with Cadogan having already sent the chopper which will be there in 5 minutes, "I pray that you're both on it." Cadogan cuts the transmission while his message alarms Grace. Grace explains to Callie that it means that "the missiles are in the air" and they need to get to the bunker. Though Callie questions how her father knew ahead of time, Grace states that he didn't and people all over the world are scrambling for bunkers. Grace believes Cadogan, stating that he is many things but a liar is not one of them.
As the Nuclear Apocalypse rages, Cadogan works on the Anomaly Stone, stating that there are only two symbols to go. Callie is angry that her father cares more about the symbols then the 11 billion people dying at the current moment, but he explains that it is the key to saving the human race, Cadogan having found and stolen the Stone from a hidden observatory beneath the Temple of the Sun in Machu Pichu. Cadogan is convinced that the Stone was sent to Earth to save the human race, stating that there were seven symbols on the temple wall and they know that they need seven symbols to chart a course through space. Cadogan attempts to activate the Stone, but nothing happens. Grace urges Cadogan to speak to his scared people, insisting that they need to set an example for the Second Dawn leading to an argument between the family before Cadogan agrees that Grace is right. Reese tells his father that 92% of the Level 12's made it to the bunker in time, giving them 1,104 people. Cadogan orders the 8% of resources stockpiled in case something goes wrong, but Callie takes off.
Two years later, Becca Franko arrives on Earth from Polaris and Cadogan has the bunker locked down to prevent anyone from knowing of her arrival. Becca finds herself drawn to the Anomaly Stone and Cadogan allows her inside the room after realizing that the Anomaly Stone is causing Becca's symptoms. Commenting that "music is mathematics," Becca is able to activate the Anomaly Stone, opening the Temporal Anomaly. Becca introduces herself to Cadogan who tells her to call him Bill. Cadogan is shocked by Becca's immediate success as he tried for years with nothing, but Becca comments that given the number of symbols, that's not surprising without an instruction manual. The Cadogans and Becca argue about what to do next and Becca offers to alter the blood of everyone in the Second Dawn so that they won't have to survive underground or risk a trip through a wormhole. Cadogan instantly refuses, arguing with Callie about it who points out the number of people who have committed suicide over the last six months. However, Cadogan is only further convinced that the Anomaly is their only hope with both Reese and Grace agreeing with him. "I've never been more sure of anything in my life," Cadogan asserts.
Callie later tells Becca, who has closed the Anomaly out of fear that Cadogan will throw her through it, that her father has always been stubborn but now believes that he can walk on water after being worshipped for two years and won't change his mind. However, Callie believes in Becca instead and wants to give Nightblood to everyone in the bunker behind his back.
Shortly after Becca activates the Stone, causing it to turn into a ball of light that she disappears into, Cadogan arrives. Before he can touch the light, Becca returns and insists that she must shut down the Stone. Becca insists that if Cadogan saw what she did, he would let her shut it down. Becca states that she has seen Judgment Day and what they have experienced isn't it. Becca insists that none of them are ready for what's coming, especially not Cadogan and has he Reese stop Becca from touching the Stone and imprison her until she changes her mind. Callie lies that Becca was gone when she arrived and insists that Becca was sent there to save them. However, Cadogan tells his daughter that he will save them, not Becca and orders Callie to get out which she does, taking Becca's Nighblood serum with her.
After Reese discovers the existence of the Flame from Becca's notebook, Cadogan decides to burn her at the stake if Becca won't tell him the final code to open the Anomaly in order to gain the Flame for himself. After Becca refuses a final time, the cult, led by Reese, burns her at the stake while Becca attempts to convince Cadogan's followers that he's killing them, not saving them.
After the execution, Cadogan sees Callie leading people injected with Nightblood to leave the bunker. Cadogan orders his men to stop them, but Grace seals the inner hatch so that they can get away. Cadogan turns to Reese, only to learn that Callie has the Flame. However, Callie gave her brother Nightblood and Reese promises to chase after her and get it back and Tristan promises to join him, having been made a Nightblood by Becca in order to save his life. Opening the airlock, Cadogan finds it empty while Grace insists that they have to let Callie go. Cadogan hugs Grace before suddenly shoving her into the airlock where Grace protests that she will die as she doesn't have Nightblood. Walking past his shocked followers, Cadogan orders them to get the Flame back at all costs. Cadogan then leads the remaining cultists through the Anomaly to Bardo.
In the present, Cadogan begs Clarke to tell him if Callie is still in her head. Clarke tells him that Callie is, "but that's not how it works," pointing a gun at him. Cadogan asks how it does work, but Clarke states that he killed her best friend so she doesn't really want to help him. Cadogan begs Clarke who orders him to bring her other friends to her immediately, but he states that he can't give orders to men who are not there. Holding Cadogan at gunpoint, Clarke has Gabriel open the door and he orders her friends sent in. Apparently fully converted into Disciples, they enter.
In The Flock, Anders asks a group of Disciple children about the Shepherd's time on Etherea.
In A Little Sacrifice, Clarke demands that Cadogan release her friends, but he states that they are not his prisoners. Clarke offers him a deal: she will use the Flame to help him after he lets all of her people return to Sanctum. Cadogan agrees, but Echo states that they aren't going anywhere as they have a war to fight with Diyoza and Octavia agreeing with her. Turning on Cadogan, Clarke demands to know what he did to her friends, but Anders states that they didn't do anything to them, her friends are merely ready to serve the cause, to fight the last war which Cadogan states will soon be upon them now that Clarke is there. Clarke demands to talk to her friends alone before she helps them which Cadogan agrees to against Anders' objections. Clarke demands that Cadogan stay with them however, an order which Cadogan reiterates to Anders who reluctantly leaves. Clarke has Miller hold Cadogan at gunpoint against the far wall while she, Niylah, Gabriel and Jordan discuss the situation.
Left alone with Jordan, Niylah and Gabriel, Cadogan comments that Callie must've been important for her language to survive for so long. Niylah tells Cadogan that Callie is remembered as brave and strong, so much so that even her enemies mourned her death. Cadogan starts to ask what Callie's title means, but changes his mind. Gabriel comments that he remembers Cadogan different and questions how he survived for so long. Cadogan states that it was "cryogenics. Plus a well-balanced diet." Cadogan recognizes Gabriel from Anders' story as someone like him: immortal, from Earth and worshipped as a god by his people. However, Gabriel states that he lost his way for a time and never actually believed that he was a god. Cadogan tells Gabriel that they are all gods and are all on a journey to transcendence even if they took different paths which Gabriel states does sound like him. Cadogan enjoys talking to someone from the same time period as him and admits that he did used to be different and has changed over the centuries.
When Gabriel questions what Cadogan has learned, he shows the group logs left behind by the native Bardoans that the Disciples found and translated over the course of centuries. Cadogan draws their attention to a translation of the part of the logs talking about the Anomaly Stone becoming like a star which leads to the last war and transcendence. However, the Bardoans didn't record the code which is why the Disciples need Clarke to find it. Cadogan believes that when the last war is won, they will see an end to violence and true peace which is refuted by Jordan and Niylah. Cadogan welcomes them to read the logs while he gets lunch, leaving. Gabriel stops Jordan and Niylah from shooting Cadogan as they will lose their leverage and, taking Jordan's gun, promises to bring Cadogan back after lunch.
Gabriel joins Cadogan in the dining room where the two men exchange banter about the food and their history as self-made men. Cadogan insists that the Second Dawn was not a cult and he doesn't claim to be a god, nor does he even believe in God. Cadogan states that he does believe himself to be chosen and that they will learn who when they win the last war. Cadogan is sure that they won't lose the war and states that Gabriel can thank him when they save him or he can join them. Gabriel questions what Cadogan is fighting for if he is cutting out everything that makes them human and Cadogan in turn questions if Gabriel has ever done anything that he regrets in the name of love. Recognizing from Gabriel's reaction that he has, Cadogan states that they all have and they all fight for whatever they have to so that their side can survive. However, being betrayed by someone they love is the worst pain that there is which is something that the Disciples don't have. Gabriel tells Cadogan that he can't fight a war for the soul of the human race with an inhuman army, but Cadogan doesn't believe that it matters in the long run and all that matters is what comes next and believes that the answers they are both seeking about what comes next are finally in their grasp.
Their meeting is interrupted by Anders and Disciple guards before Gabriel can answer if all of that is worth a little sacrifice. Cadogan thanks Gabriel for his company and orders Gabriel escorted back to his friends. Once Gabriel is gone, Anders tells Cadogan that they have a problem.
At the same time, Jordan examines the logs closer and based upon his knowledge of the Korean language, believes that Cadogan mistranslated it. Instead of a war, Jordan believes that there is a test to determine the fate of the human race, something that makes more sense. Upon hearing this, Gabriel decides not to share it with the Disciples, stating that Bill Cadogan is the wrong man to undergo such a test when the code is found.
In Etherea, Bellamy and Doucette follow the path of Cadogan's pilgrimage across Etherea in order to reach the Anomaly and escape. Bellamy becomes annoyed by Doucette's constant mentions of the Shepherd, but while they take refuge in the Cave of Ascent where Cadogan took shelter for three months during a blizzard, Bellamy finds the picture of Cadogan's family which he had left behind on the planet. They also find the glowing beings in the cave who are the proof that Cadogan had found of his beliefs. After Doucette states that "from the ashes we will rise", Bellamy asks for the picture back and realizes that Bill Cadogan is in fact the Shepherd. Having seen a video of him preaching while on Earth, Bellamy calls Cadogan a cult leader, a fraud and a con man, but Doucette defends Cadogan as the man who had predicted the Earth's destruction and led the Disciples safely to their new home across the stars.
After Bellamy questions what Cadogan believes in, Doucette explans that Cadogan believes in the bond that unites them all, that everyone is connected and offers to show it to Bellamy. Bellamy reluctantly agrees and prays to the Shepherd, causing him to experience a vision where he encounters Cadogan alone in the cave which now has weapons sticking up out of the ground. Cadogan leads Bellamy towards the inner cave where the beings are located, but Bellamy states that he has already seen what is inside. Gesturing to the weapons surrounding them, Cadogan states that Bellamy is wrong that they can save him and calls faith "the true weapon." Cadogan tells Bellamy that he has come far and his eyes are opening, but there is still much more for Bellamy to see. Cadogan leads Bellamy into the inner cave where a vision of Aurora Blake appears and Cadogan vanishes.
After Bellamy and Doucette return to Bardo from Etherea, Cadogan greets them personally and Bellamy kneels before Cadogan and addresses him as "my Shepherd." Cadogan puts a towel around Bellamy's shoulders and has him stand and asks to be called Bill. Cadogan is excited by the return of Bellamy and Doucette as pilgrims from Etherea and wants to know everything. However, Cadogan tells Bellamy that his friends are there and they've gotten themselves into some trouble.
Accompanied by several armed Disciples, Doucette and Bellamy, Cadogan visits Clarke's group in his personal quarters which he had given to them. Clarke has decided to pretend to help the Disciples in exchange for Cadogan letting her friends go back to Sanctum, but they are interrupted by the return of Bellamy. The Disciples prevent Octavia from hugging her brother, but Cadogan allows Clarke to due to Clarke having the Key in her head. Cadogan expresses hope that Clarke is ready to help them now that Bellamy has returned, stating that too much blood has been spilled and each death is a child of Earth who won't Transcend. Cadogan begins leaving to give them time to reunite while the Disciples make preparations, but Bellamy stops him. To everyone's shock, Bellamy, now completely loyal to the Disciple cause, reveals the truth to Cadogan that the Flame has been destroyed.
In The Stranger, Cadogan despondently examines the Anomaly Stone, commenting that they had been so close. Gabriel attempts to comfort Cadogan who accuses Gabriel of lying to him that Clarke had the Flame. Gabriel points out that Octavia's memories had done that, not Gabriel and the Disciples had simply failed to see the moment the Flame came out. Cadogan states that Gabriel let him believe that before they are interrupted by Bellamy asking for a moment alone with Gabriel. Cadogan agrees and orders everybody else out of the room and Gabriel locked up with everyone else.
Cadogan realizes that Bellamy is wondering what will become of his friends and invites Bellamy to sit with him at a table. Bellamy offers his condolences to Cadogan for the loss of Anders, assuming that they were close. Cadogan states that he actually only met Anders twice with each First Disciple usually awakening him every 20 years to state that there has been no progress with the last war. Anders was the only one to wake him twice, the second time because they had found the Key. Cadogan agrees that "comparatively speaking", they were close, but recognizes that Bellamy was merely testing him with the question. Cadogan states that he doesn't want to cause Bellamy anymore pain, but his friends have to pay for their actions since dozens of Disciples are dead due to their actions. Bellamy asks about potentially fixing the Flame using the technology on Bardo with Cadogan realizing that he will only help him get it if Cadogan doesn't hurt Bellamy's friends.
Cadogan tells Bellamy that Bellamy reminds him of his son Reese. Cadogan states that Reese went in search of the Flame and Cadogan never saw him again. As a result, Cadogan suspects that Callie killed Reese but he'll never know for sure. Bellamy suggests that if they can repair the Flame and Callie really is inside, they can find out for sure. Cadogan agrees that Bellamy's friends will be absolved provided that they can get the Flame, repair it and if it contains the last code.
Later, Cadogan oversees Clarke in the M-Cap where she fights the memory extraction. Bellamy suggests that Clarke honestly doesn't know, but Cadogan believes that she does or she wouldn't fight so hard against them. Cadogan orders it turned off and the first of Clarke's friends sent to Penance. Clarke finally agrees to take Cadogan to the Flame but only once all of her friends are safe which he agrees to before leaving the room.
Cadogan leads Clarke to the Stone room where her friends are still restrained and Clarke explains their deal while demanding to know why they haven't been released. Cadogan states that he has trust issues where Clarke is concerned due to her earlier lies and has Doucette remove the restraints one at a time, warning that "any violence will be met with lethal force." Bellamy assures Cadogan that no one is getting violent as they are being released and Cadogan opens the Anomaly. One by one, Clarke's friends don Disciple helmets in order to keep their memories and travel through the Anomaly.
However, Cadogan closes the wormhole without letting Raven or Gabriel go through. Cadogan explains that he is ensuring that Clarke keeps her part of the deal while Raven, having watched him, realizes that Cadogan didn't send the group to Sanctum. Cadogan confirms this, stating that it is why he didn't send Raven with them while Gabriel explains that Raven knows how the Stone works. Cadogan points out that he only promised that Clarke's friends would be safe and said nothing about releasing them on Sanctum. Only Cadogan knows where they are and he doesn't trust Clarke, but he does trust the love she has for her friends. Cadogan promises that once he has the Flame and the last war begins, her friends will all be freed at which point they will all be welcome to fight alongside the Disciples and if they choose not to, the Disciples will save them anyway "that is what we mean when we say for all mankind."
Cadogan, Gabriel, Clarke, Raven and Bellamy travel through the Anomaly to Sanctum where Clarke is shocked to find Sheidheda in charge and wonders what has happened.
In Blood Giant, Gabriel approaches Sheidheda, wondering what is going on. The Dark Commander demands to know who Gabriel is and Clarke realizes that it isn't Russell. Otis introduces Sheidheda and Raven comments that they now know where his code went. The Dark Commander demands that everyone either kneel or die, but Cadogan informs him that while he normally would relish the opportunity to recruit Sheidheda's forces to the cause, he has neither the time nor the patience to do so at the moment.
On Cadogan's signal, cloaked Disciples kill the Dark Commander's Wonkru guards, allowing Raven, Indra and Clarke to rush to help the tied-up Murphy. Murphy comments that he can accept invisibility and ray guns, but he needs an explanation for Bellamy's new status. Clarke asks if Madi is safe with Gaia, only to learn that everyone else had thought that Gaia was with her. Murphy reassures Clarke that Madi is safe for now and Cadogan orders Indra restrained with Sheidheda against everyone's wishes. Cadogan points out that Indra was standing by the throne and states that the only reason she isn't dead is that she was unarmed. Sheidheda charges Cadogan, but a still-cloaked Disciple stabs him in the gut. Cadogan has a Disciple bring the palace's microphone over and the the Dark Commander that his wound is deep and Cadogan has no interest in removing Sheidheda from his throne. Cadogan proposes that the Dark Commander gives him undisturbed passage to get what he came for, meaning that Cadogan sees not a single soul on their path and in exchange, Cadogan will leave Gabriel there to treat him. Once the Disciples are gone, Sheidheda is free to "continue the debasement of our species" until he is saved along with the rest of humanity once Cadogan completes his quest although the other option is for the Dark Commander to die. With Sheidheda agreeing, Cadogan orders the others that it's time to go after the Flame.
Outside, Cadogan derisively observes the state of Sanctum, but monologues about how thanks to the Disciples, humanity will transcend and reach the Promised Land, much to Clarke's annoyance. Clarke begins leading the group through Sanctum and Murphy approaches Bellamy, believing that he is only playing along with the Disciples and asking what his plan really is. Bellamy informs Murphy that it isn't an act and that it's real and he is trying to save them all. While Bellamy doesn't expect Murphy to understand, Bellamy tries to reassure Murphy that he is still Murphy's friend and Bellamy is looking out for him. Not at all reassured, Murphy walks away from Bellamy, much to his distress.
As they make their way through Sanctum, Cadogan suddenly orders the group to stop and Clarke tells him that she's in a hurry and that he has their friends and she would like to have them back and then to see her daughter. If Cadogan would like to see his, he has to follow her. Cadogan announces a new plan: Clarke goes while everyone else stays there. Bellamy objects, reminding Cadogan that as long as their friends are out there, Clarke won't risk their lives. Cadogan states that that's why Raven and Murphy are staying with them and orders Clarke to hurry along as Cadogan doesn't want to be on Sanctum for any longer than he has to be. After looking at Bellamy for a moment, a frustrated Clarke walks off alone. Murphy suggests waiting in the tavern, but is stopped by two armed Disciples decloaking in front of him. Raven tells Murphy that he will get used to it and the two exchange quips about how well the other did as Cadogan, Bellamy and Doucette settle onto a vantage point to keep watch.
As Raven and Murphy sit and talk around a campfire, Bellamy watches his friends and reassures a worried Doucette that Clarke will be there soon. Cadogan turns to Bellamy and acknowledges how hard the whole situation is on him, "believing in something with all your heart that the people you love don't understand." Cadogan states that Bellamy reminds Cadogan of himself when he was young and he asks Doucette to excuse them which he does. Cadogan muses that Doucette is a good man who will make a fine replacement for Anders, but he isn't like Cadogan and Bellamy. Bellamy is confused by Cadogan's meaning and he explains that the Disciples are taught their ways from birth and they know nothing else which makes faith easy. On the other hand, Cadogan and Bellamy know the pull of love between individuals, what it makes them do, the highs and lows of it, how it leads to hatred of the other and tribalism. Cadogan has spent generations dedicating his life to something greater, transcendence, which Bellamy now knows the weight of as well. Cadogan states that the "path of the Prophet is always hard" and Bellamy's friends will all understand eventually. Bellamy asks how Cadogan managed it with his family as Bellamy feels like he's failing both Cadogan and his loved ones. Cadogan reassures Bellamy that Bellamy isn't failing him and Bellamy is special. Like Cadogan, Bellamy was given a glimpse of what comes next, but Bellamy worries that his friends all think that he's crazy. However, Cadogan intends that they will save them anyway and will ignore everyone else's judgments "for all mankind" which Bellamy agrees with.
Suddenly, alarms begin going off warning that Red Sun toxin has been detected. Murphy and Raven join the Disciples and Bellamy urges Cadogan to get back to Bardo for his own safety. Cadogan refuses to leave without the Flame and suspects that it might just be another one of Clarke's tricks. Raven draws everyone's attention to the sky where the gas giant that Sanctum orbits has been turned red by the eclipse and affected bugs are attacking Sanctum's shield. The power goes out as people begin rushing for Ryker's Keep and Murphy suggests that they should join them unless Bellamy wants to drown him again in the pond. Raven realizes that the power being out means that the shield is down and spots a swarm of affected bugs coming towards them. Raven urges everybody to run which Bellamy agrees with, but Cadogan refuses to leave without the Flame. Doucette agrees that they should execute the hostages and get Cadogan home which Murphy points out isn't what Bellamy had said. Bellamy states that Clarke heard the alarm too and will go for Madi who Murphy states is in the reactor. Raven agrees that it's perfect as she can get the power back on and kill the bugs before the bugs kill them. The Disciples, Raven, Murphy and Bellamy all grab a torch and race towards the machine shop and the reactor.
The group arrives just after the swarm has killed Knight and two other members of Wonkru who were trying to break into the reactor. Using their torches, the group drives off the swarm and seals up the machine shop on Bellamy's orders in order to keep them out. Clarke arrives carrying a bag before they can finish sealing off the machine shop and explains that it contains anti-toxin from the farmhouse. Cadogan realizes she wants to use it on Madi, but Clarke states that there's enough for everyone, although Clarke was thinking of her daughter before Cadogan. Everyone takes the anti-toxin and Cadogan calls it "another lesson in the destructiveness of familial love." Clarke tries to get through the locked door to the reactor without any success and Cadogan questions if she got the Flame or not. Clarke promises that if Cadogan gets her through the door, she will give it to him without a fight. Cadogan agrees and has Disciple Kelly blast open the door. After everyone is reunited, Clarke hands the Flame over to a pleased Cadogan.
While they wait for Raven to restore the shield, Bellamy stands with Cadogan and Doucette as Cadogan examines the Flame and Madi warns Clarke that she shouldn't have given Cadogan the Flame based on the memories of the Commanders inside of her head. Cadogan asks Bellamy how long they have to stay there and Bellamy states that once the power is back on, the bugs will kill each other and the shield will prevent any more from coming in. However, until then, it's not worth the risk. Bellamy walks away from the Disciples and is embraced by a pleased Emori who is not yet aware of his defection. Bellamy admits that it's good to see her too and Emori comments on his clothes and Murphy pushes Bellamy to explain himself. However, the power returns and Bellamy decides to wait for another time and walks away, telling Cadogan that it won't be long now, shocking Emori when Bellamy addresses Cadogan as "my Shepherd."
With the shield restored and the bugs gone, the Disciples, Bellamy, Clarke, Murphy, Emori and Raven make their way to the Great Hall where an armed Indra, having dispatched the Disciples left behind by Cadogan to guard her and Sheidheda, demands to know where her daughter is. Cadogan is confused as to who Indra is talking about and Bellamy tells Indra that nobody even knew that Gaia was missing until that day. Bellamy promises that they will get everybody back and orders Indra to put down the gun which Indra does after Clarke confirms his order. Urged on by a hallucination of Josephine Lightbourne, Gabriel reveals that he believes that he can repair the Flame's damaged code using a computer designed to repair broken Memory Drives, stitching together broken strings of code that, like the Flame itself, was created by Becca Franko. Cadogan gives Gabriel the Flame who inserts it into the computer and states that if Becca's memories are still inside, the computer will find them. The computer successfully begins repairing the Flame's code, but Gabriel suddenly changes his mind and destroys the Flame completely with a gunshot. Gabriel turns his gun onto Cadogan and orders the Disciples to take off their helmets and drop their weapons which they comply with. As Gabriel takes the anti-toxin, Bellamy attempts to calm him down, stating that they need Cadogan to get their friends back, including Echo and Hope. Taking advantage of Bellamy distracting Gabriel, Doucette attempts to attack him only to be shot in the chest by Clarke. Horrified, Bellamy catches Doucette who urges his friend not to lose faith before dying.
With the situation under control, Clarke orders Raven to fire up the Anomaly Stone so that they can get to their friends. Using a Disciple helmet, Raven is able to reactivate the Stone and demands to know which planet their friends are on. Cadogan informs Clarke that the planet if off-line and only he knows the code to it. Checking the star map, Raven determines that Cadogan is telling the truth and that there is one planet that they can't get to. Clarke demands that Cadgoan enter the code in exchange for getting to live and he complies, opening the Anomaly to their missing friends. Cadogan states that they have the Bridge to their friends, but Clarke orders Cadogan to come with them and he tells her that she should have more faith. As Bellamy approaches, Clarke orders him to remain behind as Bellamy has made his choice while Murphy really hopes that what he believes in was worth it. Bellamy asserts that it was and Raven leads Murphy, Emori, Jackson, Madi and Gabriel through the Anomaly with no one else saying a word to their former friend. Clarke leaves Indra to cover Cadogan while she approaches Bellamy and tells him that while Clarke had said that she wouldn't lose anybody else, she has: she's lost Bellamy. Clarke doubts that "Disciple Blake" even cares and with a parting shot of "so much for together", sends Indra and Cadogan ahead of her through the Anomaly.
As Cadogan and Indra leave, Sheidheda offers Bellamy his help in exchange for help in return and directs Bellamy to the sketchbook containing Madi's drawings of the Commanders' memories. Unable to convince Bellamy to not turn it over to Cadogan, Clarke reluctantly kills him, but is forced to flee through the closing Anomaly without the sketchbook.
In A Sort of Homecoming, Clarke's group discovers that Cadogan has taken them to the Second Dawn Bunker on Earth. Cadogan declares that the bunker is perfect for them and holds up a pill that he identifies as being from the nano-tracking program. Swallowing the pill, Cadogan tauntingly tells Clarke "what is it you say? May we meet again." As Clarke raises her gun to him, Cadogan vanishes in a white light, escaping back to Bardo.
However, the group discovers that Cadogan really did take them to where he had sent the others. After reuniting and discovering that the Earth has in fact regenerated from the Second Nuclear Apocalypse, Murphy suggests finding the Anomaly Stone to leave, but Jordan tells the others that they couldn't find the Stone. Gabriel asserts that there must be one since it was how Cadogan got his people out centuries earlier and Raven uses her helmet to locate the Anomaly Stone 100 feet straight down from the fighting pit. When Jordan states that the group couldn't use their helmets to find it, Raven explains that Cadogan had the Disciples give them trash helmets so that they couldn't escape. Unwilling to lose anyone else that she cares about, Clarke smashes the helmet so that the group has to remain on Earth.
On Bardo, Cadogan examines Madi's sketches, particularly one of Callie, while waiting for Sheidheda to regain consciousness. When the Dark Commander wakes up and complains about his restraints, Cadogan tells him that he is lucky that the Disciples brought Sheidheda to Bardo at all. Showing the Dark Commander a sketch, Cadogan asks if he drew it, but Sheidheda admits that while he didn't draw it, he does know who did. Cadogan warns the Dark Commander that while their medicine is incredible, so is the Disciples' ability to dig through his memories for answers. Wanting to save time, Cadogan asks what Sheideheda wants and the Dark Commander asks for assurances that Sanctum will be his, that they will destroy the Stone and that the Disciples will never return. Amused, Cadogan states that the Anomaly Stones are indestructible, but Sheidheda is welcome to have Sanctum for himself.
Cadogan is sure that the Dark Commander can't comprehend what the sketches mean, but Sheidheda knows that it means that someone has memories not their own, memories that Cadogan needs to start a war with whomever created the Stones. The Dark Commander wants no part of the war, content with having just Sanctum and Cadogan clarifies that it is not a war but the last war and Sheidheda will be a part of it whether he likes it or not. Cadogan explains that if they win, humanity will transcend, evolving beyond their mortal forms and becoming one with a universal consciousness. Although the Dark Commander prefers his new body over the idea, Cadogan tells him that transcendence will be better and whether or not Sheidheda fights with them, he will still transcend as will every member of the human family. The Dark Commander condescendingly wishes Cadogan luck and asks if they have a deal or not. Cadogan calls him a fool as, if they lose, it won't matter what planet Sheidheda is on or whether or not he fights: every human dies if they lose. The Dark Commander reveals that Madi is the one who holds the memories of the Commanders and Cadogan realizes that Bellamy knew too and that was why Clarke killed him.
As Cadogan gets up to leave, Sheidheda warns him that Clarke will never let him take her child. Cadogan makes it clear that he won't be asking and the Dark Commander knows that Cadogan will no doubt send a strike team to get Madi. However, he warns Cadogan that Clarke's group will no doubt fight back, Madi included and points out that if Madi gets killed in the process, Cadogan will be left with nothing. Intrigued, Cadogan asks if he has a better idea and Sheidheda suggests sending him instead. Cadogan is doubtful as the Dark Commander wants no part of this, but he tells Cadogan that he now knows what's at stake, "transcend or die" and he knows that with that, there's not much of a choice. Having been inside of Madi's head, Sheidheda is confident that he knows Madi better than she knows herself and asks how well Cadogan's strike team knows her. The Dark Commander promises to get her back in exchange for their deal standing. Accepting Sheidheda's offer, Cadogan releases him from his restraints and orders the Disciples to take the Dark Commander to the Anomaly.
Not wanting to transcend, Sheidheda attempts to kill Madi instead of bringing her to Cadogan. However, Indra and Gaia manage to defeat the Dark Commander who is forced to flee back to Bardo. Octavia warns that Cadogan will send more Disciples after them and Raven is able to use Sheidheda's damaged helmet to discover that the Anomaly Stone is somewhere in the bunker's rec room. With Gabriel having been killed by Sheidheda, Madi, unwilling to risk the lives of anyone else that she cares about, uses the locator tag left behind by the Dark Commander to willingly send herself to Bardo. Once Madi is on Bardo, Cadogan and the Disciples send a bomb through the Anomaly to the bunker, but Miller manages to contain the explosion by placing the bomb in the hallway. However, the bomb causes parts of the bunker's hallways to collapse.
In The Last War, Cadogan enters the code and arrives on a pier he once took his daughter in the middle of a star field. Taking the form of Callie, the Judge appears to Cadogan who realizes that Clarke and her friends were right all along about the test. However, as he begins to take it, Clarke shoots Cadogan through the back of the head, killing him. She then shoots him several more times in the back.
Despite Cadogan's death, the test has already begun and can't be stopped. In the form of Lexa, the Judge's first question for Clarke is why she killed Cadogan when he was unarmed and no threat to her. Clarke justifies it as being because Cadogan killed Madi, but the Judge reminds Clarke that Madi is not yet dead and questions Clarke prioritizing her need for revenge over the fate of the human race. Clarke calls Cadogan's death justice, not revenge but the Judge states that its still "blood must have blood."
After being returned to the Stone room, Clarke discovers that Cadogan's dead body has been returned, it having disappeared between Clarke killing Cadogan and speaking with the Judge. Spotting it and the look on Clarke's face, Raven comments that it can't be a good sign. Later, when Clarke returns to Sanctum after humanity achieves Transcendence, Cadogan's corpse is still lying on the floor in the Stone room where it's abandoned by Clarke.
After Clarke finds that she is the only one who didn't Transcend, she returns to Earth where the Judge explains that Clarke can never Transcend as she murdered Cadogan during the test.