Kaworu makes his way down to where Rei IV called for him. But before he rendezvous with her, he notices something off. He can hear her Song before he even sees her, and notices that her Song, while familiar, seems different. Like the missing pieces in place of the one he knows. Confused but still eager to see her, he continues onwards. He meets up with her, and she greets him, then lashes out with her AT-Field.
Already somewhat on guard, he raises his own AT-Field in defense, asking why she's attacking him. She replies that he's an Angel, and she must kill Angels. Kaworu pleads with her, asking what's happening, but she just repeats that she has to kill him. Deeply hurt and confused by the apparent betrayal, Kaworu's Angelic side starts to take over. Losing ground as he tries to restrain himself, he pleads with Rei to stop, asking if she remembers everything they've been through up to that point. She only replies that he needs to die. Heartbroken and desperate, he lets Tabris take over, and lashes out. Rei IV is left dead, as Kaworu stands over her. Filled with grief, he makes no attempt to resist as Tabris begins to guide him to his destiny.
Furious at Rei IV's failure, Gendo immediately calls on Asuka and Hikari to prepare for engagement, claiming the 17th Angel is active and heading to the Geofort's lowest levels. Hikari responds in the affirmative, if nervously, but Asuka is skeptical. She demands to know where Rei and Misato are. Gendo makes up an excuse about where Misato is, and claims that Rei is dead, killed by Kaworu. Asuka calls him a liar, but rather than threaten to punish her, he has the security footage of Kaworu killing "Rei" shown on her Eva's HUD. Furious about this perceived betrayal, Asuka and Hikari spring into action with their Evas.
As Kaworu is making his way down to Lilith's chamber, he internally laments that it's come to this, how despite all the differences from the other timelines, it ends up the same way again, with him going to initiate Third Impact, and everyone trying to stop him. While internally reminiscing about how much he enjoyed his time, he begins to hear a familiar Song, faint and growing fainter, but one he immediately recognizes. As he begins passing by Akagi's lab, he sees the original Rei's Song from within. Confused, and suddenly hopeful, he desperately wrests control of his body back from Tabris, staggeringly moving away from Lilith and towards the Song. He finds himself in front of the LCL cylinder with an unconscious Rei laying inside. Not sure what's happening, but relieved to see her, he smashes the cylinder with his AT-Field, sending glass and Tang everywhere. Watching as Rei's fading Song starts regaining strength, he walks over and cradles her.
Rei hazily wakes up to find herself being held by Kaworu, who's shaking so hard she imagines he's going to vibrate out of his skin. She says his name, to which he pulls back to look at her with tears in his eyes. She asks him what he's doing there, to which Kaworu shakily explains what happened. As she listens, Rei angrily notes that Gendo must have had another clone hidden away, and he must have used her soul fragment from the destroyed Unit-00.
Despite being somewhat wobbly from what Fuyutsuki had tried to do to her, she gets to her feet and grabs her clothes. Kaworu asks what they should do next, to which Rei replies they need to head to Lilith's chamber. Kaworu is shocked by this, as he had just used all his strength to avoid going there, and he was still at risk of starting an Impact. Rei replies that Gendo is making his move, and to have any hope of stopping him, and SEELE, they need to silence his Call. Kaworu protests that he's still reeling from seeing her die by his hand, but Rei simply kisses him, reassuring him that she'll be there with him. Somewhat relieved from her kiss, he agrees to follow her. The two then head out of the lab.
They try the elevator but it doesn't respond. Rei figures that NERV must have shut it down to hinder their movement. She then uses her AT-Field to pry the doors open to the shaft. Looking at Kaworu, she asks if he can use his AT-Field to float them down safely. When Kaworu says he's not sure, given his still shaken state of mind, Rei then proposes he can carry her bridal style, hoping the arousal will keep his Call silent. While taken aback be this, Kaworu nervously agrees. Taking Rei in his arms, he begins slowly descending down the shaft, with Rei offering words of comfort the whole way down.
As the two of them near the bottom of the shaft, they notice that Asuka, Hikari, and their respective Evas are waiting in front of the bottom set of doors. Rei comments that Asuka's light suggests that she's especially angry. Kaworu replies that Asuka probably thinks he killed Rei. Figuring Asuka might think he's carrying her corpse in their current arrangement, Rei tells him to let her down on her feet as they reach the bottom so she can stand in front of him. He obliges, and then uses his AT-Field to pry the doors open. As Rei steps out, Unit-02 launches an AT-Field covered punch, only to pull back when Asuka sees it's Rei. Shocked but relieved that her friend is seemingly alive and well, Asuka asks what's happening.
As Rei tries to explain, Gendo interrupts them, ordering the two Pilots to kill the 17th Angel. Asuka, predictably, ignores him and again asks Rei to explain things. Gendo reminds her that he's given her a direct order, to which Asuka asks why she should listen to him since he clearly lied about Rei being dead. Gendo replies that he is the Commander of NERV, that he also thought Rei was dead (technically true), and Kaworu is still an Angel and needs to be eliminated. Asuka again refuses, to which Gendo orders her Eva be deactivated, though Asuka's mother prevents any signals from going through, forcing command to wait for her batteries to drain. He turns his attention to Hikari, ordering her to kill Kaworu. Asuka counters and insists that she wait and listen to what Rei has to say. Gendo again warns about the consequences of insubordination, and insists that Tabris will destroy the world if he continues to live. Confused, conflicted, and overwhelmed, Hikari asks her mother what she should do. Having spoken with Kaworu previously, and believing him to be a good person, Hanako suggests that they should hear Rei out. When Gendo starts threatening Hikari again, her mother blocks the connection to the command center.
Knowing that Asuka's batteries are running out, Rei hastily explains that the Rei they saw die was an emergency backup clone that Gendo had stashed away. When Hikari asks about why Rei has clones, Asuka tells her not to worry about it, and she'll fill her in later. Rei then explains that she and Kaworu need to get to Lilith so she can fix him. When Hikari asks how that'll work, Rei says it's complicated, but if it works, it'll make it so that he doesn't feel compelled to destroy the world. Hikari asks if it will control his "other side" (something her mother suggested based on her conversation with Kaworu), which Rei confirms.
While this is going on, Gendo and Fuyutsuki are quietly conversing, wondering what Rei hopes to accomplish. Gendo comments that she's clearly in league with Misato and the others. As they listen to the technicians wondering why the Evas won't respond to their command signals, Fuyutsuki silently wonders if the spirits within the Eva Cores are the cause, and begins to think that what Misato said about talking to the souls may be true. When he asks Gendo about this, the Commander responds that they'll get their answers soon enough. Fuyutsuki then muses that he knows exactly what Gendo is thinking about. Gendo then calls the Section 2 head and orders him to be ready to arrest the four Pilots and bring them to his office. He also orders that Misato, Akagi, Kaji, and Shinji be brought as well.
After hearing Rei's explanation, and despite being worried about what awaits her and the others afterwards, Hikari agrees to help her friends. Asuka laments that her power is about to go out, so she asks Hikari to do what Rei says. Rei asks Hikari to hold her and Kaworu together in her hands and carry them over to the white giant, much to the horror and confusion of the command squad. Hikari spreads her Eva's hands out so Rei and Kaworu can stand on top of them, lifts them up, and carries them both over to Lilith. As they get closer to the progenitor, Kaworu becomes increasingly agitated, so Rei encourages him to hold her close. She asks Hikari to hold them close enough to Lilith for Rei to touch her, which Hikari complies with. Rei instructs Kaworu to open his plugsuit/remove his top (I'm not sure what he's wearing at this point). He shakily complies, and Rei reaches out to Lilith. Using her AT-Field, she extracts a small globule of material from Lilith, then turns and tells Kaworu to loosen his AT-Field, which he does. Rei then proceeds to push the globule into Kaworu's now permeable chest, while a grossed out Hikari turns her head away. After a few seconds, Rei extracts her hand, and Kaworu falls limp in her arms. She calls his name several times, then calls him a stupid fish, at which point he jerks back up with a gasp. She then asks how he feels, to which he replies that it feels "so quiet." He confirms happily that the incessant voice in his head has gone silent. The two hybrids share a joyous embrace. Kaworu than asks what happens next, to which Rei responds that they need to face the Commander.