In From the Ashes, some of the Disciples arrive through the Temporal Anomaly from Bardo and kidnap Bellamy Blake. Three are taken down by Echo and one of their HUD's identifies Gabriel Santiago and Echo with orders to capture and not kill them and to take the two back to Bardo. However, they are under orders to kill Hope Diyoza on sight. One, wounded but still alive, attempts to kill Hope, but is shot dead by Echo. With the Anomaly closing, presumably done by the remaining kidnappers to keep anyone from following them, Gabriel, Hope and Echo chase them through the Anomaly together.
In The Garden, Hope, Gabriel and Echo arrive on Skyring where Hope explains that the Disciples then used the Anomaly to travel to Bardo. However, while Hope has the code for the Anomaly Stone on a paper she kept in her arm, the code was washed away, keeping the group from traveling on to Bardo. Hope believes their only chance of reaching Bardo is in five years when they come back for their current prisoner, though with the time dilation, this would likely be a shorter time on Bardo. Exploring Doctor Colin Bensen's Memory Drive, Gabriel discovers that Colin figured out the code for Bardo, but his computer is destroyed before they can record it.
In a flashback, ten years after Octavia Blake and Charmaine Diyoza arrived on Skyring, a team of Disciples arrive through the Anomaly from Bardo, having received a message in a bottle Octavia had tossed into the Anomaly in the hopes of it reaching Bellamy. The Disciples kidnap the two women and presumably bring them to Bardo.
In Hesperides, Gabriel, Echo and Hope ambush five Disciples and steal their suits, using the Anomaly to cross over to Bardo.
In Welcome to Bardo, shown in a flashback 45 days ago, Octavia and Diyoza arriving on Bardo after being kidnapped from Skyring. Anders, the leader of the Disciples assigns a scientist named Levitt to look through Octavia's memories to retrieve any information that she has on Clarke. He spends 3 days looking through Octavia's memories, and becomes infatuated with her, to the point where he agrees to help Octavia get back to Skyring so she can find Hope. Hope arrives from Skyring and plans to send Octavia back to Sanctum and then retrieve Diyoza. Levitt plants Hope's location tracker on Octavia's back so that she can find Hope once she returns to Sanctum. Levitt opens the Anomaly and sends Octavia back to Sanctum, with her arriving back only a few moments after she originally left Gabriel. In a flashback to 7 days ago after Octavia is returned to Bardo, Levitt is taken off Octavia's case as Anders worries he is getting too close to her. Anders proclaims that Bellamy has arrived and they need Octavia to help talk him down. Bellamy is seen holding one of the guards at knifepoint near the Anomaly Stone. Octavia agrees to tell Anders everything about Clarke if he sends Bellamy back to Sanctum. Anders agrees and go to open up the portal, but one of the fallen guards detonates a grenade, seemingly killing Bellamy. In the present time, Gabriel, Echo and Hope arrive on Bardo and find Octavia in a catatonic state with another scientist. After watching the memory of Bellamy's supposed death, Echo becomes enraged and brutally stabs the scientist to death.
In Nakara, Gabriel, Echo, Hope and Octavia attempt to head to the Anomaly Stone so that they can return to Sanctum. On the way they run into Diyoza, who has escaped her confinement. When they reach the room containing the Anomaly Stone, they encounter Levitt, who is now working as a janitor. Levitt tells Octavia that the Disciples are waiting in the room, and will kill themselves to make sure the others do not escape. He instead suggests that they take the route through the oxygen farm to the outside surface, as the Disciples will not follow for fear of death. When the group arrives at the door to the oxygen farm, Gabriel blocks their entry, claiming it too much of a risk, due to the surface's uninhabitable conditions. He uses his suit weapon to stun the others, and when the Disciples arrive they knock out Gabriel.
In The Queen's Gambit, Gabriel is offered a job by Anders to join the Disciples code-breaking team, as he has knowledge on the Anomaly and might be able to help them unlock it's secrets. He accepts and takes the job. Meanwhile, Octavia, Echo, Diyoza and Hope find themselves in cells, where they talk, Echo and Octavia bonding over the supposed loss of Bellamy and Diyoza and Hope conversing about Diyoza's past. Echo realizes that the Disciples are not holding them hostage, but rather that they wish for the four to join their fight. The four agree to join, and are released by Anders, who promises to make Disciples of them. 3 months later, Gabriel and the code-breaking team are studying the Anomaly when Clarke, Raven, Jordan, Miller and Niylah arrive from Nakara. They are glad that Clarke had arrived, citing her as the "key". Gabriel also informs the group that Bellamy is dead. Elsewhere, Anders goes to the sepulcher chamber within Bardo, and awakens the "Shepherd", who is revealed to be Bill Cadogan, the leader of the Second Dawn cult from before the first nuclear apocalypse.
In Anaconda, Anders meets with Clarke's group, explaining that the Key that the Disciples are searching for is the Flame. In flashbacks, its revealed that Cadogan had discovered Earth's Anomaly Stone in South America's Machu Picchu a decade before the Nuclear Apocalypse but couldn't decipher the code for Bardo until Becca Franko, assisted by the Flame, helped him. After rejecting Nightblood as an alternative, Cadogan led his people through the Anomaly to Bardo to start anew. In the present, Clarke tells Cadogan that Callie is still a part of the Flame. Clarke however is un-cooperative to help since the Disciples killed Bellamy, and orders Cadogan to send in her other friends. Under Cadogan's orders, Octavia, Echo and Diyoza enter, having all seemingly been reconditioned as Disciples.
In The Flock, in a flashback to three months prior, Anders takes Echo, Hope and Diyoza to Bardo's surface to show them the crystalized remains of the native Bardoans and warns that the Gen-9 still present on the surface can calcify a human from the inside. The three are trained as Disciples while Levitt reveals that the Disciples have managed to isolate a small amount of Gen-9 though they would never use it as a bioweapon as just that small amount could kill them all. Its revealed that the enemy the Disciples are preparing to fight is the same enemy that wiped out the Bardoans.
In A Little Sacrifice, Clarke, Raven and Miller meet with Octavia and Diyoza and learn that they are only pretending to be with the Disciples to find a way off Bardo. Echo frees Hope from her cell, and tells her that she has a plan to get revenge for Bellamy, and instructs Hope to get their friends off planet within 1 hour. In the stone room, Jordan and Niylah realises that the Disciples have wrongly decoded the last message, and rather than referring to a "last war", the message instead refers to a test that must be taken by one individual representing a species. As Hope regroups with everyone else, she informs them that they need to get off Bardo within 45 minutes. From Levitt, they learn that Echo is planning on releasing Gen-9 into Bardo's central humidification system to kill the Disciples. They intercept Echo moments before she releases the virus, and manage to talk her down. As they prepare to leave, Anders appears with dozens of Disciples. Diyoza gives Anders back the Gen-9 vile, and he sentences Echo to 20 years penance on Skyring. Hope kills Anders, and then takes the vile containing the Gen-9 to release it into the system, and as a single droplet is release, Diyoza catches the droplet. This causes her body to crystallise, and she dies.
In Etherea, Clarke, Octavia, Echo and Gabriel are being held under "house arrest" within a cell. Clarke tells the others that she is going to agree to help Cadogan, in exchange for sending everyone else back to Sanctum. As Clarke prepares to leave, Cadogan and several Disciples enter. Clarke tells Cadogan that she is ready to help him, but then Bellamy enters, having just arrived from Etherea. Clarke hugs him and tells him that she is bluffing about having the Flame, and tells him to say nothing. However, as Cadogan prepares to leave to make preparations, Bellamy tells him that Clarke has been lying and that the Flame was destroyed, proving his allegiance to the Disciples.
In The Stranger, Bellamy makes a deal with Cadogan to deliver him the Flame in exchange for Cadogan not harming his friends. Bellamy pleads with Raven to tell him where the Flame is, and when she refuses he has her sent to M-Cap. He goes to Clarke and Octavia and asks Clarke the same thing, and she also refuses, so he sends her to M-Cap as well. In M-Cap, they are unable to break into Clarke's mind, and so Cadogan orders the first of her friends to be sent to Penance. Clarke tells Cadogan that she will take him to the Flame, but only if everyone else is sent back to Sanctum first. When preparing to leave for Sanctum, Cadogan instead sends Octavia, Echo, Hope, Jordan, Niylah and Miller to Earth, and promises to release them once he has the Flame and the Last War has started. With their deal set in place, Clarke, Cadogan, Raven, Gabriel, Bellamy and Doucette cross over to Sanctum.
In The Last War, Clarke kills several Disciples guarding the Stone room, but discovers that Cadogan has already entered the final code into the Anomaly Stone. On a pier in the middle of a star scape, Cadogan meets with the Judge in the form of his daughter who reveals that Jordan was right and achieving Transcendence requires passing a test, not winning a Last War. The native Bardoans had failed the test and were annihilated as a result like many other species before them. As Cadogan begins the test, Clarke kills him from behind, but is forced to continue the test herself. Clarke ultimately fails the test and the Judge, in the form of Lexa, decides that humanity with be destroyed like the Bardoans.
At the same time, Wonkru and the Eligius Prisoners arrive in the oxygen farm where Jordan Green is able to disable the Disciples' weapons and cloaks. Wonkru and the prisoners enter into a standoff with the Disciples in order to buy time for Echo and Raven to help Clarke. Raven decides to continue the test, but the Judge, in the form of Abby Griffin, uses the increasingly tense standoff between the Disciples, Wonkru and the prisoners as proof that humanity doesn't deserve transcendence. Sheidheda opens fire on the Disciples, provoking a battle between the two sides before Indra finally kills the Dark Commander. Stepping between them, Octavia talks them down and convinces both the Disciples and her own people that if they fight and destroy each other, they aren't worthy of transcendence. Both sides stand down and Raven is able to change the Judge's mind. As a result, the Judge transcends every remaining human who is still alive, aside from Clarke.
With humanity having transcended, Bardo is left abandoned once Clarke leaves for Sanctum and then for Earth.