After revealing herself to Murphy and offering him immortality, Josephine asks Murphy for more details on how Abby turned Clarke into a Nightblood. Murphy also trains her how to act like Clarke to fool Abby and everyone else. In return, Josie promises to wipe out Kaylee's family Mind Drives and give some to Murphy. Their conversation is interrupted when they hear Madi screaming.
Josephine, pretending to be Clarke runs into Madi's room where she finds Gaia watching over Madi. Gaia explains that Madi is communing with the other Commanders including Sheidheda, the "Dark Commander." She warns that Sheidheda is getting too strong for Madi and they need to do the Separation Ritual soon. Josie wakes up Madi against Gaia's advice. Gaia becomes worried that pulling Madi out like that could mess with her mind or cause the Flame to malfunction. Madi kicks both of them out. Soon after, Gaia's fear becomes a reality when Madi then sees Sheidheda in a mirror.
Raven, Echo and Emori return to bar lounge and are furious to learn what the Primes have been doing to Nightbloods. Josie defends the Primes, claiming that they've all done things they regret but Raven disagrees. Echo asks where Bellamy is and Josie lies to her that he went out to scout for locations outside Sanctum. Echo goes after Bellamy while Raven and Emori go to the machine shop.
Worried about Bellamy, Murphy asks if Josie has killed him but Josie reveals that she locked him up after discovering she's not Clarke. Josie orders Jade to go after Echo while she and Murphy figure out how to stop Bellamy from getting revenge. She says that if Bellamy doesn't side with them before Echo returns, they will have to kill him. So, Murphy pretends to be captured and thrown into the same room as Bellamy. While in there, Murphy begs Bellamy to not retaliate but Bellamy vows to kill them all and take over Sanctum. As Murphy insists, Bellamy becomes suspicious that he might not even be the real Murphy. Murphy reveals that he pretended to be captured to convince Bellamy to take a deal: do not retaliate and in exchange, the Earth group would be allowed to live peacefully in Sanctum. Bellamy refuses to take Murphy's deal.
In the machine shop, Ryker, Raven and Emori are going over the plans of making a radiation shield. Raven seems really upset with Ryker, which makes him realize that she has figured out what the Primes do. Raven says that as someone who has lived in pain for years, she understands the desire to want another body; but not if it comes at the expense of murdering another person. Ryker disagrees, claiming that it isn't murder because the hosts are willing. Raven counters by pointing out that the Primes raise people to believe that they're gods so they can sacrifice themselves. Ryker explains that he didn't choose to be resurrected - Russell killed them when they were kids; but since then he's been brought back 8 times. Raven is disgusted. She is even more offended when Ryker reveals that he keeps gifts given to his hosts, claiming to honor them. Despite Ryker acting like a good guy, he refuses to answer when Raven asks him if that will be his last body.
Out in the woods, Octavia and Diyoza continue their search for Xavier and the old man. After entering into the cave, they think they're alone when suddenly, they found Xavier. He notices that Octavia is suffering because her hand got exposed to the temporal flare. He says that he can save her. Otherwise, she only has three hours before the dilation spreads to her brain. Diyoza goes with Xavier to retrieve the cure. On the way, Xavier explains who the Children of Gabriel are. He also reveals that "the old man" is indeed the original Gabriel Santiago, the thirteenth Prime. After a moral awakening, Gabriel stopped caring about immortality and became a terrorist to fight fellow Primes. Xavier asks Diyoza to work with them for redemption instead of working for Russell to kill Gabriel. Xavier says that Diyoza's child would be mistreated in Sanctum it won't be a Royal Blood. However, Diyoza is fine with that as long as the child gets to live.
Xavier's cure turns out to be tree sap. Diyoza doesn't believe him at first but it heals her own injury. So, they put some tree sap in the bottle and take it back to Octavia. However, the cure doesn't work on Octavia. Instead, Octavia's arm starts spiraling. Xavier gives her a stone to draw by letting the hand move freely. Octavia draws a logarithmic spiral and Xavier says that it is the shape of The Anomaly - the source of the temporal flare. He says that the temporal flare was a message that the it is calling her. He then reveals that he has the same spiral on his chest. Diyoza then opens her book, revealing similar spirals. So, Octavia, Diyoza and Xavier agree to go together to the Anomaly.
Back in Sanctum, Madi is terrified as she continues to see the Dark Commander whenever in the mirrors. Gaia hears her screaming and comes to check on her. Upon realizing that it is the Dark Commander taking control, Gaia suggests performing the Separation Ritual right away. The Ritual is used to call upon the other commanders to confront Sheidheda. As the ritual begins, Gaia advises Madi to focus on a good memory; and Madi chooses the day she first met Clarke. Madi starts chanting. After a while, she finds herself in a big room with no one else but Sheidheda. The Dark Commander tells Madi that Gaia is lying to her just like his own teacher lied to him. He says that Gaia wants to control Madi. He reveals that he killed his own teacher and tells Madi that she should kill Gaia as well. Madi refuses and wakes up from the memory only to find that Gaia has chained her up. Madi wants to break away but Gaia forces her to go back in and repeat the ritual a few more times.
After learning how to be Clarke from Murphy, Josie goes to Abby and asks about the Kane problem. She mentions that the Primes can save Kane if he was a Nightblood. She explains that they would have to download Kane's brain into a Mind Drive and install it into another Nightblood. Abby is reluctant at first but Josie convinces her by telling her that they've all done horrible things to survive; and that Kane deserves to live. Josie says she's worried about losing her because she's afraid of what Abby might do if Kane died. Abby agrees and asks Raven to fly her to the mother ship.
Josie reveals the news to her mother, Simone and asks her to erase the Kaylee's family Mind Drives and give some of them to Murphy and Abby as an incentive to embrace the Nightblood program. She convinces Simone by saying that it is a small sacrifice they have to make for the other Primes to be assured of a steady supply of hosts. Simone agrees and erases the Lee's family Mind Drives. Josie gives two of the Mind Drives to Murphy.
Meanwhile, Echo joins the rest of the crew in hopes of finding Bellamy. She consults her map and deviates from the crowd to look for Bellamy elsewhere. On her way, she finds a man tied up by tree vines, with some vines going right into his body. The man asks for mercy and Echo figures out that he's asking her to kill him instead of dealing with the pain. She lifts a rock to kill him but Jade appears from the bushes and stops her. Jade explains that the man was a Sanctum guard who lowered the shield on the day and he chose that punishment because he is the one who opened the shield the day that Rose got kidnapped. When the man continues to beg Echo for mercy, Echo knocks Jade out and kills the man. She then ties up Jade in the same spot instead. As the vines start to penetrate under her skin, Jade begs Echo to let her go. Instead, Echo asks why she's following her. Since Clarke is the only one who knew where Echo would be, Echo easily figures out that that wasn't really Clarke. She asks about Bellamy and Jade explains that Bellamy is locked up but will be killed by the time they return home. So, Echo abandons Jade in the vines and goes back to Sanctum to save Bellamy.
Bellamy is sitting in his room as he sees the Gagarin fly off. Josie goes to kill Bellamy but her father and Murphy arrive to stop her. Russell begs Bellamy for forgiveness for what they did to Clarke but Bellamy doesn't accept it. When Bellamy gets free, he grabs Russell and tries to kill him. Josie tells him to do it but asks for the cycle of blood to end there. Since this echoes what Monty and Clarke had been saying, Bellamy feels guilty and decides to let Russell go free. Russell, Josie and Murphy convince Bellamy to not get revenge for Clarke's "death." Bellamy agrees and is set free. He reveals everything to his friends and personally delivers the bad news to Madi. He hugs Madi to comfort her.
Grieving from losing Clarke, Madi goes back to her room and Gaia follows her. Sheidheda reveals himself to Madi and pressures her to kill Gaia. Instead, Madi banishes her from Sanctum. Madi then asks Sheidheda how to kill everyone.
Later that night, Josie goes to bed, proud of her success that day. As Josie falls asleep, Clarke wakes up trapped in Josie's mind and is revealed to be alive. She seems to be in her cell on The Ark, and on the walls are drawings of some of the people who have had impact in Clarke's life. She starts struggling to figure out where she is and how to get out.