She is first seen off panel, using Evangelion Unit 01 to attack the Third Angel. After this skirmish she is seriously wounded, confusing many in NERV when Gendo Ikari calls for a defensive against the angel. Misato claims it took Rei seven months to synchronise with her Eva. When she is brought out, Rei is on a dripline with bandages on her arms and face. Despite her condition, she agrees to pilot Eva 01 again. Rei is still being tended to after Shinji’s battle.
Rei is enrolled in the same school as Shinji, and seems to be doing better since the battle. Her arm is in a sling, and she still has bandages over her face though. When Suzuhara tries to fight Shinji, Rei looks on from a window. She is seen again later during a second attempted-fight between the pair and tells Shinji there’s an emergency. Misato mentions to Shinji that Eva 01’s systems will be rewritten for Rei when Shinji decides to leave NERV, and this is later authorised by Gendo.
Rei bumps into Shinji and tells him that, if he had quit, she’d have done a good job piloting Eva 01. Misato tells him she’s like that with everyone. Ritsuko mentions that Gendo Ikari burnt his hands in Eva 00’s activation test. Shinji thinks that’s where Rei was injured. During the test her entry plug was ejected, and Commander Ikari opened the hatch with his bare hands. His glasses cracked in this incident, and Rei keeps them as a memento. Shinji comments that Rei’s past is mostly a blank.
She talks to Gendo in the cage about Eva 00’s reactivation test. Shinji muses that his father would never look or talk to him like that. He later goes to see her and give her a new security pass, but she had just finished having a shower. He fell onto her and she didn’t react, merely getting dressed and asking him to leave the card on the table. The pair travel to NERV headquarters together, and she tells Shinji the only thing she has faith in is his father.
When Shinji awakes after the failed attempt to attack the Fifth Angel, Rei is at his bedside with food waiting to brief him on the coming battle. She explains to him the timetable, also adding that if he wasn’t willing to go through with the operation Eva 01 could be rewritten so that she could pilot it. She pilots Eva 00 in the Mt Futago battle in a defensive role, using a shield to protect Eva 01 from the angel’s particle beam weapon.
Before the battle, Rei explains she pilots Eva because it’s her ‘link’. After the angel fires once at Eva 01, Rei steps in with her shield to deflect the second shot. After her shield melts, Rei uses Eva 00 itself to save Eva 01 and buy Shinji more time. Shinji then tries to rescue Rei from Eva 00, saving her in much the same way his father had earlier.
Rei is with Shinji, Misato and Ritsuko watching recorded footage of Unit 02 defeating an angel at sea. Afterwards, Rei tells Shinji that she was aware other countries were producing their own Eva’s. She is soon introduced to Asuka at NERV headquarters, but doesn’t seem to hold much of an opinion of the new pilot. Considering Eva 00 being out of commission, Rei doesn’t appear as often compared to the functioning pilots Shinji and Asuka. She is allowed to watch some of their special dance training however, and is asked by Misato to step in for Asuka at one point to practice the dance with Shinji. When they perform the dance in harmony, Asuka runs out of the room.
Eva 00 is reconstructed after her disastrous battle with the Fifth Angel, yet Rei is involved in a test with Unit 01. Her synch ratio is said to be the same in both units, and Gendo believes this means they can implement ‘the plan’ sooner - to have a 'dummy' program modelled on Rei's personality as a back-up for the Eva's pilots. The activation takes all evening, so she misses school. Shinji goes to her place to give her the work she missed out on, and she invites him in for tea. While there Shinji asks her how to talk to his father, and Rei suggests just telling him what he feels.
She is involved in the Eva-run to catch the angel falling from orbit, and uses her progressive knife to slice open the angel’s AT field. After the mission the headquarters suffers from a blackout. Due to her knowledge of the base’s layout, Rei assumes leadership and points Asuka and Shinji towards the command centre. She is seen again, stabbing a white giant called ‘Adam’ with the Lance of Longinus that was found by Commanders Ikari and Fuyutsuki at the south pole.
She is next seen in a cylinder of sorts, with Ritsuko mentioning that Rei’s personality has been used for the Dummy Plug. Rei is present at the battle against the Eva 03 angel (labelled the Eighth Angel). When Shinji tells her who the pilot of the corrupted Eva is, she noticeably hesitates to fire upon it.
Rei talks with Asuka about Shinji’s state after the battle with Eva 03. She is later sorties in Eva 01 but is rejected. Taking matters into her own hands, Rei pilots Eva 00 and attacks the angel with an N2 bomb. Her attempt to destroy the angel fails. She awakes in the hospital some time after the battle.
She asks Gendo Ikari if he’s going to be by Eva 01’s side, but he says that he doesn’t have to be there. Rei leaves, realising that the void in her heart has been filled by Shinji. When it looks like Shinji plans on staying in the Eva, Rei tries to call out to him to return. When he does, she is happy. Rei seems to be developing greater feelings for Shinji, asking at one point if she could hold his hand.
Rei is later seen receiving a shot from Ritsuko. Ritsuko snidely comments that Rei has both Gendo Ikari and Shinji wrapped around her finger before attempting to strangle her, but the older woman backs down and apologises immediately. Rei is warned to watch what she says.
During the battle with the Tenth Angel, Rei fires using a positron rifle but can’t break through it’s AT Field. Gendo suggests using the Lance of Longinus to defeat the angel, ordering Rei to collect it from Adam’s body. She throws the lance and kills the angel. Some time after the battle she meets Kaworu Nagisa, who says that they are the same. Rei disagrees with him.
She is sortied with Kaworu during the battle against the Eleventh Angel. Her Eva is contaminated by the angel, however.
While Rei’s Eva is contaminated, she is able to speak with the angel. It tells her that she has been jealous of Shinji’s attention to Asuka in her comatose state. She cries at this knowledge as her Eva’s contamination worsens. When Eva 01 is released to rescue her but starts being contaminated itself, Rei inverts the AT Field of her Eva in order to contain the angel. Her last thought before the Eva is destroyed is of Gendo Ikari.
Some time later she is revealed to be alive, albeit again in bandages. She tells Shinji that she probably doesn’t remember saving him from the Eleventh Angel because she is the third. When she sees Gendo’s glasses in her apartment she is confused when she begins to cry, claiming that this is the first time that she’s seen them.
A younger Rei appears in Ritsuko’s flashbacks, where Ritsuko’s mother Naoko notices a resemblance between her and Yui Ikari. A couple of years later she is strangled to death by Naoko Akagi. Ritsuko calls this Rei the first.
Ritsuko reveals that Rei was raised within NERV, and that there are countless clones that can continue to hold her soul. This reveals that the Rei killed by Naoko was the first vessel, the Rei seen throughout the series the second, and the new Rei is the third.
Rei encounters Kaworu, who tells her that they have both arrived in the bodies of humans to live on the Earth. During the final angel’s attack on headquarters, Rei uses her own AT Field and follows the fight down towards the white giant Adam, who Kaworu claims is in reality Lilith.
After Kaworu’s death, Gendo mentions that SEELE's attempt to use Kaworu to initiate Third Impact would have been incomplete without the Lance of Longinus and the most essential part - Lilith's heart. Fuyutski turns to Rei as this is said.
She is seen in the Dummy Plug plant, examining the bodies of her dead clones before being collected by Gendo.
When she and Gendo arrive in Terminal Dogma, Rei witness Ritsuko Akagi’s attempted betrayal and death at the hands of Gendo Ikari. She watches this emotionlessly.
Like Asuka, Rei is hinted to be far more intelligent than her age (or her quiet nature) makes her appear. In the anime she is seen reading an advanced book on genetics. She also knows the layout of NERV, capable of finding and accessing every place in the facility, including sections many staff members don't know exist.
At the end of both anime series, Rei becomes the avatar of the second angel, Lilith. She becomes a god-like being that gains the ability to reshape humanity. The manga series appears to be taking steps that explore this plot, with Rei using her AT Field in Volume 11 and being referred to as Lilith's heart obliquely by Gendo.