In From the Ashes, Raven is concerned by her inability to trace Sheidheda's transmission. After Madi starts drawing memories that are not her own, Clarke questions if they are Sheidheda's, but Gaia suggests that they might belong to one or all of the other Commanders instead.
After Clarke knocks Russell Lightbourne unconscious, he awakens in a Mindspace resembling the room Sheidheda and Madi met in. Sheidheda, having downloaded himself into Russell's Mind Drive, comments that he likes Russell's current host better than his original body. Stating that he is now Russell, Sheidheda slits the Prime's throat from behind, killing him.
Sheidheda regains consciousness, now fully resurrected in Russell's final host. By playing on Clarke's emotions, he is able to get her to save "Russell" from the fire engulfing the Sanctum palace. However, as Sheidheda revels in his resurrection, Clarke announces that Russell Prime will be executed for his crimes the next day.
In False Gods, Sheidheda, still posing as Russell, is mentioned to have been visited by many of Russell's remaining followers. Looking through a book, Sheidheda enjoys the sensations of having a body again before being visited by Clarke and Indra who announce his execution at sunset. Given a choice of executions, Sheidheda decides on burning at the stake so that Russell's followers will be forced to witness it as will Clarke.
Later, concerned that the Adjusters are planning something drastic, Jordan Green visits "Russell" for help. Sheidheda rejects food, stating that it will all turn to ash anyway and wanting to die and facing it are two separate things. Jordan begs Sheidheda to help "his" people who are planning some kind of an attack to stop the execution which will lead to people dying. Sheidheda simply tells Jordan to tell them not to kill him, surprising Jordan by his lack of caring. Jordan tries to convince Sheidheda to go out doing the right thing, using his voice to stop his people from dying. Sheidheda suggests that he ask his people nicely and Jordan says that he won't be asking by his father's son before leaving.
Jordan convinces the others to bring "Russell" out to address his people, though Indra threatens to kill him herself if he doesn't say what he's supposed to say which Clarke warns Sheidheda. Sheidheda states that they both want the same thing, peace before addressing the crowd. Sheidheda tells the crowd that if his death is needed to bring peace, then so be it and urges them not to take action as Clarke is right that they are all that's left of the human race. Declaring Sheidheda to be a false god, a man tries to kill him, but only succeeds in shooting Sheidheda in the shoulder before being beaten down by the crowd. As chaos breaks out, Clarke and Eric Jackson tend to Sheidheda's gunshot wound which damaged his subclavian artery. As he's taken off to Medical, Indra asks if Sheidheda will survive. Clarke believes so and Indra states that she hopes he does otherwise "Russell" will become a martyr to the fanatics and without Wonkru to keep the peace, Sanctum will explode. Clarke reluctantly realizes that they can't kill him which Indra confirms.
As Jackson treats his wound, Sheidheda questions if something is wrong. Jackson asks if he even cares about the people he's killed and Sheidheda states that his list of regrets is a long one before being interrupted by Indra. Indra informs Sheidheda that his execution has been cancelled as Russell's followers will burn Sanctum to the ground if they go through with it. The Dark Commander knows that they don't have the forces to stop it, pointing out that some of his guards are gone. One of Russell's followers warned of the attack and so is allowed to see Sheidheda as the fanatics no longer trust Jordan. The woman secretly tells Sheidheda that he had been right about Jordan who never suspected and did exactly what Sheidheda said he would while the shooter, Tobin, is dead. Pleased, Sheidheda enjoys the cookie she brought as the woman leaves.
In Welcome to Bardo, after one of Russell's followers, now calling themselves the Faithful, commits suicide, Indra asks Sheidheda how it feels to know that his people are willing to die for his freedom. Sheidheda claims that it feels awful and offers to talk them down again, but Indra decides to have John Murphy, still posing as Daniel Lee, do it instead.
As the Faithful are about to burn Murphy alive, Sheidheda enters with Indra and Emori, slapping Trey for his audacity and threatening Zev. Sheidheda calls himself, Daniel and Kaylee the last of the Primes and claims to love Murphy like a son as Murphy saved his life. Sheidheda orders Murphy's release, before turning and berating the Faithful for trying to sacrifice themselves for his sake when their uprising had stayed his execution as they are the only thing keeping him alive. Sheidheda demands that everyone kneel or die which they do, but it causes Indra to realize Sheidheda's identity. In Trig, Indra tells Sheidheda that there is a spider on his shoulder and he replies in kind that its too bad she can't kill him. Indra orders "Russell" escorted back to the lab.
Indra confronts Sheidheda, finally knowing what happened to the Dark Commander's code when they saved Madi. Sheidheda simply states that they both know Madi was too weak to be the Commander and asks if Indra's parents knelt when he conquered Trikru. Indra reveals that her father died in the battle, but her mother did kneel when it was over and Indra thought her weak for it. Indra states that when the people riot for the loss of their god, she plans to personally slit the Dark Commander's throat. As several people, including Nelson enter, Indra states that she may not be able to kill Sheidheda just yet, but she can make sure that he won't come back when she does kill him. Indra has Jackson painfully cut out Russell's Mind Drive so that the Dark Commander can never resurrect again.
In Nakara, Sheidheda emerges from his cell, much to Indra's fury. The guard explains that he is allowed outside for ten minutes every day, but the fact that the guard was talking to Sheidheda causes Indra to dismiss him as Sheidheda predicted. Indra orders that only Trikru is to guard Sheidheda who is not to speak to anyone and if he does, they are authorized to "shut him up." Indra changes her mind and instead orders that the Children of Gabriel guard the Dark Commander due to the risk of them being seen speaking with the enemy leader.
After dismissing the guard, Indra makes it clear to Sheidheda that he has no rights, but he is unconcerned, responding in Trig that he is recovering fine and he enjoyed resurrection and would've enjoyed the chance to be able to do it again. Indra states that the moment Sheidheda stops being useful, she will kill him herself. The Dark Commander mocks the number of people Indra has on her side and the theft of Wonkru's guns. Sheidheda states that what Indra needs is a Commander, but claims that Madi is broken. He suggests that Clarke could potentially lead as she once bore the Flame which only 3 people alive can claim to have done. The Dark Commander knows that Indra is afraid that Wonkru will choose to follow him, commenting that he would be too if Sheidheda was her. Furious, Indra leaves without another word while Sheidheda gives her a mocking nod.
Sheidheda is examining a chess figurine when Nelson enters, initially mistaken by the Dark Commander for Indra. Not satisfied with the Dark Commander being unable to resurrect, Nelson attacks, attempting to kill him. However, he proves to be no match for Sheidheda who easily overpowers and disarms Nelson. After winning the fight, Sheidheda helps Nelson up, stating that if he really had been Russell, he has no doubt that Nelson could've killed him. Sheidheda reveals to a shocked Nelson that he is not Russell Lightbourne and that he had killed Russell and taken over his body. Sheidheda offers to help Nelson get power, revealing that Wonkru is weak and the Eligius prisoners most likely have the guns. Sheidheda convinces Nelson to ally with himself to get power, stating that he has to first make allies with the prisoners "and then you take out the enemy's queen."
Due to the growing threat from the prisoners and the Dark Commander, Indra attempts to get Madi to be the Commander again, but she refuses out of fear. Indra reveals to John Murphy and Emori that Sheidheda is back and they need their Commander because Sangedakru will follow him and eventually the rest of Wonkru will fall into line. Murphy and Emori convince Indra to reunite Wonkru under her leadership instead to face the threats from the prisoners and the Dark Commander.
In The Queen's Gambit, Murphy is sent to bring Sheidheda his food as Indra doesn't trust anyone else to not be corrupted by talking with the Dark Commander. Sheidheda dismisses Murphy as a mere servant boy and discovers a message from the Faithful in the cookie Murphy brought him stating "Unification Ceremony Today". Sheidheda eats the message and notes that Indra must trust him to send Murphy into the cell with him. Though Murphy states that no one trusts him, the Dark Commander knows that Indra must trust Murphy or she wouldn't have told Murphy who Sheidheda really is. Sheidheda knows that Murphy is scared, seeing through his lie that Murphy still believes him to be Russell. Sheidheda insists that Murphy doesn't need to fear him and states that being feared works better than being afraid of someone.
The Dark Commander invites Murphy to a game of chess, commenting that its nice to be able to talk to someone and not have to pretend to be Russell. Sheidheda states that he saved Murphy's life and the least he can do is indulge the Dark Commander in a game of chess. The Dark Commander offers to give Murphy what he wants most of all: a chance to be a hero. Sheidheda reminds Murphy of his heroic actions to save the child the Faithful wanted to burn and questions Murphy about being scared. Murphy finally asks how the Dark Commander can make him a hero, claiming not to care about that but knowing that Sheidheda must know something bad is going to happen to offer that. Sheidheda confirms that something bad is about to happen from Murphy and instructs him to make a move and states that people will die if Murphy loses. Murphy begins playing with the Dark Commander who comments on Murphy using the aggressive queen's gambit against him.
The two continue playing, bantering as they do with Sheidheda suggesting that as a god, Murphy could have any woman he wants and not just Emori. The Dark Commander suggests that Emori is liking being worshipped while Murphy taunts the Dark Commander about his own past and how Lexa is everyone's favorite, having united the clans. Sheidheda angrily states that he united the clans and the Flamekeepers had banded together to kill him as they were afraid of his ideas and they had killed Lexa for the same reason. The Dark Commander assures Murphy that he won't let that happen again and Murphy realizes that the Dark Commander wants to be back in power. Sheidheda simply taunts that Murphy realized what Indra already knew from the moment she realized he was alive again. Sheidheda defeats Murphy's queen's gambit and states that "there are leaders and there are followers. How you respond to the loss of your queen will tell me what you are." Murphy tells the Dark Commander that he is neither but a rebel, but Sheidheda questions Murphy's presence if that is true. Murphy tells him to just continue playing the game, but the Dark Commander states that chess is more than a game: its strategy and uncertainty governed by choices. When Murphy tries to threaten him, Sheidheda orders him to consider his words carefully, admitting that he likes Murphy, but a real survivor would carefully consider his words on the off chance that his enemy escapes and takes power. Sheidheda promises to tell Murphy what he is planning if Murphy wins the game and they continue their chess match.
As the match nears its end, both men admit that they are most dangerous when they are cornered before Sheidheda suddenly pulls back from a potential checkmate. Noticing this, Murphy realizes that the Dark Commander is only distracting him and Sheidheda explains that only Daniel's words hold water with the true fanatics, meaning that Emori's ceremony will fail without Murphy's help. Quickly overpowering Murphy, the Dark Commander holds a chess piece to his neck, threatening to kill him if Murphy makes a sound and declaring checkmate. As gunfire sounds, Sheidheda releases Murphy and states that he can call for help now. Murphy screams for help and armed guards rush in as a satisfied Sheidheda returns his king to the chessboard.
In The Flock, after taking 30 hostages, Nikki demands Murphy and Sheidheda be brought to them. Reluctantly, Murphy convinces Indra to seek the Dark Commander's help. Lying on his bed, Sheidheda mocks Indra's control over Sanctum, but she knows that he got what he wanted. Sheidheda simply suggests that Murphy go and play hero, but he states that they are both going. Sheidheda questions why he would, knowing that if everyone realizes the truth, they will tear him apart and if he survives that, they have no reason to keep him around. Indra suggests a slow death then and there if he doesn't help them, but Sheidheda states that he will need more. Indra promises to protect him from the Faithful which he agrees is a start and promises that he can have back his 10 minutes a day of guarded time outside. The two negotiate it to 20 minutes and the Dark Commander requests someone to play chess with as well, "someone who understands the complexities." Though he looks at Murphy, Murphy refuses to play with him again and Indra refuses to play games herself and to find him someone instead. Sheidheda agrees to the deal, but offers them a better plan and provides them with a map showing a tunnel under the palace leading into the Great Hall. The Dark Commander states that Alyssa can show them the way and that "I feel like this is the beginning of a beautiful friendship."
With four minutes to spare, Murphy and Sheidheda enter the Great Hall where Murphy lies that Raven took a group to the second compound site. With only a few minutes left, Murphy asks Sheidheda where the others are, but he simply states that he hopes Murphy has lots to say. Murphy and Emori reveal the truth about the Lee's being dead while the Dark Commander mockingly reveals the truth about Russell's death to the gathered crowd. As Nikki prepared to kill Emori, Murphy spoke up, stating that it was his idea to use the prisoners, not Raven's. As Murphy attempts to talk Nikki down, Indra and Wonkru invade, killing two of the Children of Gabriel and one prisoner before the rest surrender. Pleased, Sheidheda states that it went according to plan and Indra agrees that it has "so far."
In the aftermath, Alyssa questions why everyone is telling lies about him, but Sheidheda states that the others don't have the strength of her faith. Alyssa slips the Dark Commander the key to his shackles as he thanks her for leading Indra there. As Zev angrily turns on Sheidheda and Alyssa and Indra locks the door, the Dark Commander removes his sling and shackles. Taking a candlestick, Sheidheda blows out and removes the candles, mocking how lost everyone is without their leaders. Sheidheda begins mercilessly slaughtering everyone inside of the Great Hall which Indra mistakes for them killing him. Murphy quickly realizes the truth and while demanding entry, reveals the Dark Commander's true identity to Penn, Knight and the Wonkru guards. Finishing his slaughter, Sheidheda orders the door opened in Trig. The guards, Murphy and Emori discover Sheidheda standing over his slaughtered victims and the Dark Commander declares in Trig that "my fight is just beginning." Immediately, Knight and one other Wonkru guard kneel before him while Penn, another guard, Murphy and Emori remain standing.
In A Little Sacrifice, as Murphy, Emori, Indra and the faithful members of Wonkru deal with the aftermath of Sheidheda's massacre, they find the Dark Commander gone, having escaped through the secret tunnel. Knight has gone with him and Indra knows that Sangedakru will follow Sheidheda as he is one of their own and the other clans will eventually follow with more convincing as there is no alternative. Murphy, Emori and Indra realize that the Dark Commander will go after Madi, the only other alternative and rush off to get to her before Sheidheda.
Sheidheda enters the tavern where Madi is located. Several Sanctummites flee at the sight of him while Picasso growls at the Dark Commander. Sheidheda greets Madi is Trig and Madi is surprised that "Russell" speaks the language. The Dark Commander reveals that Russell is dead and that he killed Russell in the Mindspace, commenting "good thing I didn't kill you in yours." To her horror, Madi realizes that it is Sheidheda before her. Armed with a knife, the Dark Commander monologues to Madi about the quandary he is in due to Indra's influence over the remaining Grounders and Madi's lingering influence over them as a former Commander. Sheidheda demands that Madi kneel before him, threatening to cut out the hearts of everyone she loves otherwise and feed them to Picasso. Terrified, Madi complies, pleasing the Dark Commander who leaves the tavern.
Later, Sheidheda makes an announcement in Trig from the palace revealing his resurrection and Indra's lies about there being no more Commanders. Indra and Penn are unable to find Sheidheda, but hear him listing the lineage of the Commanders as he prepares to resume leadership of the Grounders. Now with a partially-shaved head and an outfit resembling the one he wore in his original body, vows to protect his people and demands that they prove that they are his people by kneeling before him. Indra interrupts, angrily stating that they will never bow before the Dark Commander. Indra challenges Sheidheda to single combat for leadership of Wonkru which the Dark Commander, pleased, accepts.
The next morning, Indra and Sheidheda, both armed with swords, engage in combat, the Dark Commander taunting Indra over giving him the chance to lead his people back to the old ways -- his ways. Indra manages to knock Sheidheda's sword into the pond, but he also disarms her. Grabbing a blade from a nearby man, Indra continues the fight through the nearby area and stabs the Dark Commander in the chest with a knife. However, he removes the knife and knocks Indra to the ground with a sword slash that leaves her seriously wounded. Indra refuses to surrender and allow the Dark Commander to take her people so he prepares to kill her.
Before Sheidheda can kill Indra, Madi leaps in and slashes him in face with knife, taking out Sheidheda's right eye. In severe pain, the Dark Commander knocks Madi to the ground and prepares to kill her, but Indra offers to kneel before him if Sheidheda spares Madi's life. Sheidheda accepts the deal and Indra kneels as Sheidheda announces himself as the Commander and threatens to kill anyone who resists while Knight ties a bandana around his lost eye. With Indra nodding at them in agreement, all of Wonkru, even Indra's loyalists, bow before the Dark Commander as their new leader while Indra passes out from her injuries.
Turning his attention back to Madi, Sheidheda finds her gone and orders Knight to find and kill her. Sheidheda leads half of his people to finish off the remaining Sanctummites, but finds them gone with only the dead left behind. Enraged, Sheidheda orders Knight to find out the names of the dead and then kill everyone in their families. Knight is shocked that Sheidheda wants the children dead too, but he justifies it as the children will grow up to get revenge if they are allowed to live. Knight reluctantly agrees and Sheidheda orders him to report back when its done. Looking at himself in a reflective piece of metal, the Dark Commander removes the bandana covering his missing eye.
In The Stranger, now wearing an eyepatch over his missing eye, the Dark Commander holds court in the Great Hall. Murphy and Emori agree to kneel before him, but Sheidheda evicts them from the palace. Emori requests that they be allowed to live in the machine shop instead with Murphy justifying it as Emori being needed to maintain the reactor and the Dark Commander not leaving his favorite chess partner to sleep in a tent. Amused, Sheidheda agrees with the request. Next, the Eligius prisoners and the Children of Gabriel enter and Sheidheda demands that they all kneel or die. Nikki and prisoners comply, but Nelson and the Children of Gabriel refuse. Taking an assault rifle, the Dark Commander kills all of the Children of Gabriel members aside from Nelson who continues to refuse to kneel. Sheidheda shoots Nelson in the head, killing him.
Later, Knight approaches Sheidheda as the bodies are removed to report that everyone else has agreed to kneel. However, Sheidheda knows that Knight really means everyone he can find and orders him to continue to search for Madi and the others, knowing that while they are currently hiding, they will want revenge and they can't have that. The Dark Commander pointedly addresses Indra, knowing that she is listening in and asks about Gaia. Knight states that Gaia is amongst the missing and they believe that she is in the woods with a group led by Clarke who are "armed and extremely dangerous." Knight reports that there was no sign of them and hands Sheidheda Madi's notebook which is open to a page depicting the Anomaly Stone. The Dark Commander recognizes it from when he had the Flame. Indra reminds Sheidheda of their deal to spare Madi in exchange for Indra kneeling to him, but the Dark Commander states that the deal was from before she went into hiding with his enemies. Indra insists that she is neither Sheidheda's enemy nor does she know where Madi is. Sheidheda orders Indra to have Trikru clean up the mess and calls Nikki over.
As Indra cleans up some of the blood from the massacre, Sheidheda stops her, telling Indra to let someone else do it. Indra simply states that he ordered Trikru to clean up the blood and she is Trikru. The Dark Commander orders her to clean herself up when she's done as the festivities are about to begin. Knight unveils a throne made out of bones for Sheidheda which he is greatly pleased with and immediately sits in. Knight has Wonkru carry in the Anomaly Stone which they have located and then reveals that Nikki, who Sheidheda had follow Indra, has gone missing but Knight took it upon himself to have Nikki followed.
Along with Knight, Indra and several members of Wonkru, Sheidheda makes his way to the machine shop where he is spotted by Murphy and Emori on the security camera. Murphy tries to pretend that he thinks the Dark Commander is Emori returning after an argument, but Sheidheda doesn't buy it and walks in while Indra informs Murphy that he already knows the truth which Murphy had already guessed. Murphy refuses Sheidheda's demand to open the reactor door, causing the Dark Commander to admit that he likes Murphy and will spare both him and Emori if Murphy opens the door. Murphy is angered when Sheidheda insultingly calls Emori frikdrena before Emori interrupts over the intercom, addressing the Dark Commander as "cyclops." Emori threatens to blow the reactor if Sheidheda harms Murphy or tries to enter the reactor room. Though Knight claims that Emori is bluffing, Murphy reminds the Dark Commander that everyone inside knows that they are dead the second they let him in meaning that they have nothing to lose. "I believe in chess that's called stalemate," Murphy quips. Stating that the game is not over yet, Sheidheda takes Murphy captive and orders Knight to wait the people out and kill them all when the door opens.
Sitting on his throne, Sheidheda plays a game of chess with a bound Murphy when the Temporal Anomaly opens and a group emerges from it including Clarke, Raven, Bellamy Blake, Gabriel Santiago and Bill Cadogan. Looking at the one-eyed Sheidheda in charge and the aftermath of his carnage, Clarke wonders what happened in her absence.
In Blood Giant, a confused Gabriel approaches Sheidheda, asking "Russell" what is going on. The Dark Commander demands to know who Gabriel is and Clarke quickly realizes that he isn't Russell. Otis announces Sheidheda's identity and demands that they bow before him while Raven comments that they seem to have found Sheidheda's code. The Dark Commander demands that they kneel or die, but Cadogan states that he has neither the time or patience and has some cloaked Disciples kill the armed members of Wonkru surrounding the Dark Commander.
As Clarke's group discusses things, Sheidheda charges Cadogan but is stabbed in the abdomen by a cloaked Disciple. Cadogan tells the Dark Commander that his wound is deep, but Cadogan has no intention of removing the Dark Commander from his throne. Cadogan offers a trade: Sheidheda gives him safe passage to get what Cadogan came for and Cadogan will get Gabriel to treat him. Once they are gone, the Dark Commander is free to continue with "the debasement of our species" until Cadogan completes his quest to transcend humanity. With the only other choice death, the Dark Commander reluctantly agrees. As Cadogan's group makes their way through Sanctum, Sheidheda makes a broadcast ordering his people to let them pass freely.
Sheidheda and Indra are tied to a pillar together while Gabriel treats his wounds. Gabriel warns the Dark Commander that if the blade hit his kidney, there's not much that Gabriel can do for him and he doubts that the Disciples will take Sheidheda back to Bardo for treatment. Indra is pleased, commenting that its time that they let the Dark Commander find out what death is like for a second time. The Dark Commander jokes that Indra will miss him when he's gone and reassures Gabriel that Russell's death was quick. After seeing a hallucination of Josephine Lightbourne, Gabriel realizes that a Red Sun eclipse is beginning and warns that they will need the anti-toxin, explaining how it works to Sheidheda. When the Dark Commander questions how he can be sure, Gabriel tells the Dark Commander that he is already feeling the effects.
Tied together, Indra and Sheidheda witness the Disciples guarding them suffer from the effects of the Red Sun toxin while Indra hallucinates her mother kneeling before the Dark Commander years before. Speaking in Trig, the Dark Commander warns Indra, who is cutting through the rope binding her, that it won't go well for them if she doesn't get them free and that "my enemy's enemy is my friend." Indra warns him that once she kills the Disciples, she intends to kill him too. As Indra continues to try to free herself, Sheidheda tells her that every time he'd take a Trikru prisoner, they'd die trying to escape and that one would think that they would get better at it.
As the Disciples arguing gets worse, the Dark Commander urges Indra to hurry. One Disciple snaps and kills another and Indra orders Sheidheda to buy her some time. The Dark Commander draws the Disciple's attention by taunting him, giving Indra enough time to break free. Indra manages to kill three of the four, but one cloaks before she can kill him. As Indra grabs a sword, the Dark Commander notices the footprints of the last Disciple in the pools of blood on the ground and shouts a warning as the Disciple sneaks up behind Indra. Thanks to his warning, Indra is able to decapitate the Disciple.
As Indra comes down from the fight, she hallucinates her mother kneeling before Sheidheda again in exchange for the Dark Commander sparing her daughter and the Dark Commander taunting Indra's mother over breaking. Taking the anti-toxin from Jackson, Indra turns on Sheidheda who points out that he saved her life and that it must be worth something. Stating that it is, Indra swings her sword at the Dark Commander's head, but stops inches from his face. Indra announces that she doesn't need to kill him as Sheidheda is already dead and cuts his face. Indra orders that the Dark Commander's wound is not to be treated which both Jackson and Gabriel agree to without hesitation. In Trig, Indra informs Sheidheda that "your fight is over."
From his position tied up, Sheidheda watches the confrontation between Clarke and friends and the Disciples that ends with the Flame permanantly destroyed and most everybody leaving to rescue their friends. Before Clarke can leave through the Anomaly, the Dark Commander weakly tells Bellamy that he can help Bellamy if Bellamy helps him. Sheidheda directs Bellamy to Madi's sketchbook on his throne containing Madi's drawings of the memories she has been experiencing from the other Commanders.
In A Sort of Homecoming, Sheidheda awakens strapped to a chair on Bardo and hooked up to an IV drip. Cadgoan, going through Madi's sketchbook, comments that the Dark Commander is lucky that the Disciples brought him to Bardo or Sheidheda would be dead. Cadgoan asks about Madi's sketches and Sheidheda admits that while he didn't draw them, he knows who did. Though Cadogan can dig through the Dark Commander's memories, he asks what he wants instead. Sheidheda wants assurances that Sanctum is his, they can destroy the Stone and the Disciples will never come back. Cadogan states that the Anomaly Stones are indestructible, but he can have Sanctum.
Cadogan doubts that the Dark Commander comprehends what the sketches mean, but he knows that it means that someone has memories not their own, memories that Cadogan requires to start the Last War, a war that Sheidheda wants no part of. Cadgoan states that Sheidheda will be a part of it whether he wants to or not because if they win, then they will transcend beyond their mortal forms. However, the Dark Commander enjoys his new body and Cadogan tells him that he will transcend whether or not he joins the fight. Sheidheda asks if they have a deal, but Cadogan calls him a fool, telling the Dark Commander that if they lose, it won't matter if he fights or not or which planet he is on as every human will die. Sheidheda reveals that Madi has the memories and Cadogan realizes that Bellamy knew and that was why Clarke killed him.
Sheidheda warns that Clarke will never let Cadogan take her child and that Cadogan's strike team could get the child killed. Sheidheda suggests that Cadogan send him instead, stating that he'd wanted no part of the fight before he'd know what was at stake: "transcend or die." The Dark Commander has been in Madi's head and feels that he knows her better than Madi knows herself while the strike team won't know Madi at all. Sheidheda promises to get Madi back, but their deal must still stand after that. Cadogan releases the Dark Commander in agreement and orders him taken to the Anomaly.
Dressed in Disciple armor and cloaked, Sheidheda emerges from the Anomaly in the Second Dawn Bunker on Earth. Though faced with Indra, Gaia and Octavia who can't see him, the Dark Commander chooses not to attack and instead to follow Octavia and then Octavia and Clarke in order to find Madi. After following the two to where Hope, Jordan, Murphy and Emori are gathered in a worshop, Sheidheda learns that Madi is in the rec room. Pleased, he shoves Octavia into the workshop and locks the group in.
As Madi and Gabriel play the piano in the rec room, Sheidheda stabs Gabriel through the back and confronts Madi. Preventing Madi's escape through a vent, Sheidheda reveals himself, telling the girl that she is the key to the transcendence of the human race and that he has been sent to bring her back though Sheidheda wants to reign, not to transcend. The Dark Commander reveals nanotracking pills he can use to bring her back peacefully, or a blade to stab her with to bring her back by force if she refuses. Drawing his suit's blade instead, Sheidheda states that he prefers to gut Madi like a pig instead. Before he can, Gabriel tackles the Dark Commander off of Madi and orders her to get help from Indra. Sheidheda stabs Gabriel several times before leaving him to die and chasing after Madi.
Sheidheda chases Madi to the bunker's fighting pit where he faces off with Indra and Gaia together. Together, Indra and Gaia manage to take down the Dark Commander and Indra goes to impale him with a sword, declaring that his fight is over in Trig. Responding "not today,", Sheidheda stabs himself with the blade containing the tracking device which he then drops. The Dark Commander vanishes through the Anomaly just before Indra can kill him.
In the aftermath of Sheidheda's attack, Gabriel dies of his wounds after refusing medical treatment. Knowing from the Dark Commander that the Disciples will keep coming for her and unwilling to risk the people that she cares about, Madi uses the blade he left behind to transport herself to Bardo.
In The Dying of the Light, Sheidheda has been imprisoned in a cell on Bardo since his return, singing the Grounder Anthem much to the annoyance of the Disciple guards sent to bring him food and Clarke who is locked up in an adjacent cell with Octavia.
After being rescued by Levitt, Clarke leads him and Octavia to the Dark Commander's cell, interrupting his singing. Sheidheda instantly realizes that they need his help since no one is shooting him and tauntingly asks Clarke what Madi would think of her actions. As Clarke begins to attack, Octavia restrains her and reminds both Clarke and Sheidheda that they need to stop Cadogan. The Dark Commander points out that he did try which is what got him locked up in the first place. Clarke admits that while she'd love to Sheidheda, they do need his help and informs the Dark Commander that they will set him loose and Sheidheda will draw the Disciples away from M-Cap. The Dark Commander refuses to be a "petty distraction" and states that he's the High King of Sanctum. Octavia tells Sheidheda that the other option is that they leave and lock the Dark Commander back up and he agrees to be the distraction.
In a hallway near M-Cap, Sheidheda draws the attention of six Disciples and announces that he is there to kill the Shepherd before walking away. Sheidheda quickly dispatches the Disciples with their own weapons and then charges six more using one Disciple as a human shield. Minutes later, Clarke, Octavia and Levitt find all 12 Disciples brutally slaughtered and no sign of the Dark Commander anywhere. Clarke points out that they knew it was a possibility that he would no longer be there and promises that they will deal with Sheidheda later.
In The Last War, when Raven argues with the Judge that Wonkru and the Eligius prisoners are only distracting the Disciples and won't attack, the Judge draws her attention to Shiedheda hidden nearby with a gun who is preparing to attack. The Dark Commander opens fire on the Disciples' position, increasing tension between the two sides. When Levitt rushes out and tries to stop the war, Sheidheda, annoyed, shoots and badly wounds the young man which Indra notices. The shooting causes fighting to break out between the two sides, a few people to be killed and Echo to be shot while helping Octavia to rescue Levitt.
After Octavia convinces Indra to order Wonkru to hold their fire, Sheidheda reveals himself, yelling that Indra is not in command but he is. Declaring "blood must have blood" repeatedly, the Dark Commander works Wonkru up into a fury and they resume firing. Sheidheda begins commanding a charge to breach the wall and kill all of the Disciples only to find Indra armed with a sonic cannon. Declaring "for my mother" in Trig, Indra blasts Sheidheda with the cannon, blowing him up and killing the Dark Commander. Sheidheda's death and a speech by Octavia succeeds in bringing the fighting to an end.