Titus continues to question Murphy, holding the ALIE chip and asking how he came to have the "holy symbol" of the Commander. Murphy tells him that it's a corporate logo and that Jaha gave it to him.
Flashback: to 97 years earlier. Becca and her assistant work on the chip, which continuously malfunctions, while aboard Polaris. Chris sends a message through from Earth, telling Becca that ALIE got out of the Faraday cage and into the system. She hacked the nuclear codes. Becca instructs Chris to get to the lighthouse bunker. Commander McAdams, the Commander of Polaris, joins them and they watch as the missiles launch from all over the globe, annihilating everyone on Earth.
Back in the present, Semet and his people bring Octavia before Lexa, interrupting Ascension Day. In private, Lexa consults with Titus and Clarke. Clarke encourages her to give the Sky People time to realize the error of their ways in backing Pike and to oust him themselves. Titus disagrees, warning Lexa that blood must have blood. Lexa calls together her ambassadors and instructs them to march on Skaikru but to only contain them, rather than attack. She enacts a kill order on anyone outside of the boundaries. Enraged, Semet calls for "Death to the Commander!" and moves to stab Lexa. Titus intervenes, killing Semet, and ominously echoes to Lexa that blood must have blood.
A badly beaten Murphy manages to escape the restraints Titus put him in and tries to escape the room. He notices ALIE's symbol and other etchings on the wall. He spots the piece of Polaris, putting together that it now says Polis and once said Polaris.
Flashback: the stations float independently in space. It is Unity Day, when Polaris is set to join the other 12 stations. On Polaris, Becca injects herself with something that looks like Nightblood. The Commander and Becca's assistant confront Becca and he demands that she stop the work she is doing. He tells her that her first AI destroyed the earth and he will not allow her to continue working on a second AI. Becca refuses to comply, insisting that ALIE 1 did not understand the value of human life but that ALIE 2 will; it will be built to coexist with humanity and humanity's needs will be its needs. She insists that ALIE 2 will be the key to saving humanity, noting that there is not enough food or air for the Ark to subsist. The Commander and her assistant disregard her and prepare to float the AI. Becca locks them both out of her lab instead.
In the present, Octavia and Clarke go to her room. Octavia asks why Indra was in the crowd and not with Lexa. Clarke tells Octavia that Indra isn't doing so well. Octavia is angry about Clarke going along with whatever Lexa says and defending her after Lexa has again left them to die thanks to that kill order. Clarke tries to explain that the 12 clans want war and this is the only way out of it. She agrees to go talk to Lexa. Octavia sneaks out of Polis.
Clarke visits Lexa. Lexa offers Clarke the option to stay at Polis as her guest, getting around the kill order. Titus speaks to Lexa privately, criticizing her for putting both herself and Clarke in danger by refusing to separate love from duty. Lexa disagrees. Titus apologizes and asks whether he can arrange for Clarke's departure. Lexa tells him that is up to Clarke.
Octavia goes to see Indra, who is weak and depressed. She begs Indra to give her guidance and come to fight with her when they march on Arkadia. Indra provokes Octavia into attacking her and then comments that she (Indra) should have died along with her people on the battlefield. Octavia leaves, angrily telling Indra she can die there or come with her and get revenge.
Titus goes down to where Murphy is being held and sees his chair empty. Murphy jumps out from where he was hiding and attacks Titus. Titus easily overpowers him. Murphy begs him off and tells Titus about the Polis/Polaris connection, though Titus refuses to believe that his faith is at all connected to the Sky People. Murphy explains the history depicted on the walls, saying that the woman depicted on the walls apparently fell from the sky after the nuclear event that led the Sky People to go up to space and after Polaris was blown up. Titus points out that the small figures around the woman were the first group of Nightbloods. He knocks Murphy out once Murphy compares the woman who fell out of the sky to the 100 delinquents.
Flashback: The Commander and Becca's assistant beg her to allow them to join the other stations, noting that Russia and China are threatening to stop docking measures and are going to make an example out of them by blowing them up if they don't get in line. Becca inserts her AI into herself and refuses, telling them to allow her to save humanity. She insists she is trying to save the human race. She takes her work and leaves Polaris via an escape pod, leaving the rest of Polaris behind to be blown up.
Octavia confronts Clarke, calling her out on Lexa asking her to stay behind. Clarke tries to suggest that she can do more for their people by staying in Polis. Octavia tells Clarke that the Sky People need her and that Pike will not obey the blockade; they need to go back to Arkadia to prevent their people from dying. She tells Clarke she is leaving in an hour and if Clarke stays, Clarke is not the person that she thought she was.
Clarke goes to tell Lexa's room to tell her that she's leaving. Lexa is not surprised and understands that Clarke needs to go back to her people. Clarke comments that "maybe someday" after the two of them have no more that they owe their people, they can be together. Lexa tells her "may we meet again." Clarke kisses Lexa and they have sex.
Lying in bed, Clarke comments on Lexa's back tattoo. Lexa tells her she got it on her Ascension Day, seven circles for each officiate who died when the Commander's spirit chose Lexa. Clarke wonders what happened to the 8th officiate, since Lexa had mentioned there were 9 at her conclave. Lexa quickly changes the subject and they have sex again.
Clarke goes back to her room to prepare to leave and finds Murphy tied up and Titus with a gun. Titus tries to shoot Clarke, planning to frame Murphy so that Lexa will perhaps be angry enough to finally declare war. Lexa enters the room and is accidentally shot by Titus.
Clarke tries to stop the bleeding, begging Lexa to stay with her. Lexa tells her not to be afraid. Titus takes out the tools that look similar to the ones used by Becca aboard Polaris. Titus asks Lexa for forgiveness. She has him promise not to harm Clarke and bids him to do his job and guide the next Commander.
Octavia prepares to leave for Arkadia. Indra joins her and they head out together.
Titus rubs some of Lexa's blood on his head. Clarke repeats the traveller's prayer to Lexa. Lexa dies. Titus convinces distraught Clarke to allow him to complete the ritual. Titus turns Lexa over and we see the sacred symbol tattooed on her neck.
Flashback: Becca reaches the ground, where the radiation level is critical. ignoring that warning, she takes off her helmet and tells the approaching Grounders that she is there to help. We see the mark on the back of her neck where she has sewed the AI into herself.
Titus cuts open the back of Lexa's neck and the AI chip climbs out. Murphy recognizes it as an AI. Titus says it is the spirit of the Commander. He puts the AI in a case, picks up Lexa's body, and carries her out. He announces that the Conclave is to begin to choose the next Commander and leaves, locking a shocked Clarke and Murphy inside the room.