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 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 its 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.