He is Shinji’s father, and the commander of NERV. Typically, he is seen seated in the ‘Gendo Pose’, his glasses shining. Ten years earlier, he left Shinji with an uncle so as to focus on his work with NERV. His dedication to the organisation is at the expense of his son, who claims that he thought his father had forgotten him. In the face of adversity he is exceedingly calm. As soon as command is transferred to NERV, he begins to exude a sense of smug authority. Gendo is confident in the abilities of the Eva series and NERV’s ability to defeat the Angels. He is ridiculously pragmatic, and seems to see humans as expendable – he calls Shinji ‘the reserve pilot’ upon his arrival at NERV headquarters.
The Eva-series is a part of Gendo Ikari’s work. Having been placed in charge of the defensive against the angel and giving command to Fuyutsuki, he goes to the hangar to meet his son. Despite their tense relationship, he still calls Shinji by his first name when asking him to pilot Evangelion Unit 01. Despite needing to defeat the angel, he doesn’t need Shinji to do anything other than sit in her. When he says that he can’t, Gendo tells him that he’s useless and should get out. He decides to use Rei as the pilot again, stating that ‘she’s not dead’. After Shinji sees her condition and agrees to pilot, Gendo smiles.
When Eva 01 goes berserker after receiving considerable damage, and later when the angel self-destructs, he seems to be pleased with the turn of events. He reports to the Instrumentality Committee after the battle, who remind him of the importance of the Instrumentality Project. He acknowledges this, and tells SEELE that the official story for the battle has already been dealt with. The cover-up makes no mention of the angels or Eva Unit 01.
He is later seen in the hospital, visiting Rei. When he notices Shinji, he ignores him.
Gendo barely appears in Volume 2. He appears with Ritsuko after Shinji’s attempt to run away and shows barely any emotion about the incident. He mentions that such a reaction was one of the scenario’s predicted. He authorises for Eva 01’s systems to be reconfigured for Rei. Through Ritsuko, he tells Shinji that he appreciated his efforts before he leaves.
He is on-site at the location the Fourth Angel died, examining it’s core. Shinji feels as if Gendo thinks it was obvious Shinji would return, and has burn marks on his hands. Ritsuko explains that it happened during Eva 00’s activation test. When the entry plug was ejected, he raced into the cage to rescue Rei. He burnt his hands on the hatch. His glasses cracked in this incident, and Rei keeps them as a memento.
Gendo speaks with Rei about the reactivation of Eva 00, asking her if she’s scared. Shinji watches this, musing that his father wouldn’t look or talk to him like that. After the reactivation test he asks for Unit 01 to be launched in order to fight the Fifth Angel.
After Misato has organised a plan to defeat the angel, Gendo and Fuyutsuki voice their amazement she was able to acquire the positron rifle from the JSSDF.
Gendo is seen collecting Adam from Ryoji Kaji after his arrival in alongside Asuka Langley Soryu. He is later shown to be displeased with the initial battle with the Seventh Angel, which causes Shinji to feel completely humiliated. He later passes Shinji and Asuka in the hall after they have begun their training, and says he is looking forward to their victory against the Seventh Angel. Gendo watches the battle with Fuyutsuki, and appears to have a smug grin on his face as the two pilots defeat the angel.
Gendo appears to have followed Kaji to an abandoned building. His motives aren’t immediately clear for why he is there. He is later seen during Rei’s synch test with Eva 01, and upon learning the results of her test calmly states that the plan can be implemented sooner. He meets Shinji at the grave of his wife, Yui Ikari, and tells him there is no body in the grave and that he should stop trying to search for him. He tells Shinji that he’s grown up and no longer needs a parent to help him, and leaves by air. These were his first, and last, words as a father as Shinji later reveals. He speaks briefly with Rei afterwards, having a much warmer conversation with her than he had with Shinji.
Just prior to the race to catch the angel falling from orbit, Shinji thinks back on some of the things he’s heard about his father; namely, that he used Yui as a guinea pig in an experiment of some kind before he abandoned Shinji. During this time Gendo is with Fuyutsuki at the South Pole, stating his belief that they can survive in its inhospitable atmosphere through mankind’s science. His purpose for being in the Antarctic was to recover a large spear.
He returns to after the black out incident that followed the angel attack, checking on the status of the Eva units.
He inspects the Dummy Plug system with Ritsuko, telling her that as long as the system convinces the Eva that a pilot is present and can make the robot move it’s ready to be installed in the Evangelions. He later talks with Fuyutsuki about the disappearance of Eva 04 at the Nevada Branch.
Gendo assumes command of the attack on the Eva 03 angel (labelling it the Eighth Angel). After Eva 00 suffers an invasion in the left arm, he orders for it to be severed, possibly to prevent a second angel from forming. After learning why Shinji won’t attack the angel, he orders Maya Ibuki to turn the Eva’s operations over to the Dummy Plug.
After the Eva 03 battle, Gendo is overseeing the attempted force-ejection of Shinji from Eva 01. He orders for the LCL compression to be at it’s maximum, sending Shinji into unconsciousness. When Shinji comes around, he sees him and charges him for criminal acts (possession of an Eva for personal use, destruction of NERV property, breaching lawful orders). After Shinji tries to hit him and quits NERV, Gendo orders for Shinji’s records to be erased and Rei to become the pilot for Eva 01.
Gendo orders for Rei to be sortied with Eva 01 with the dummy plug as a backup when the Ninth Angel attacks. When Eva 01 rejects Rei, Gendo believes that it is actually a rejection of him. After the Dummy Plug is also rejected, Gendo places Fuyutsuki in command.
He goes down to Eva 01’s cage and address the Evangelion as ‘Yui’, finding out that the Eva will only accept Shinji. When Shinji arrives asking to pilot the Evangelion, Gendo allows him. He watches Shinji’s fight, and muses when the Eva digests the S2 engine that this is the point where everything begins.
When Kaji asks him how he intends to explain the situation to SEELE, he replies that he wasn’t in control of the situation. Gendo states that until further notice Eva 01 is to be shut down.
Gendo has removed himself from the Eva 01 salvage operation, believing that Ritsuko will be able to bring Shinji out of the Eva. In the Eva, Shinji sees an image of Gendo trying to convince him to return.
He is aware that the Committee was involved in Fuyutsuki’s kidnapping.
In Fuyutsuki’s flashbacks, it is shown that he was originally Gendo Rokubungi and in love with Yui Ikari. Rumours suggest he only married her for her theories and the organisation behind her, SEELE. Gendo is also mentioned to have been a part of the Katsuragi Expedition in 2000, but left just before the Second Impact. By 2002 he had changed his name to Ikari. Yui mentions to Fuyutsuki that Gendo is sad he doesn’t like him, suggesting that he respects Fuyutsuki.
Still in flashback, he dismisses Fuyutsuki’s allegations that he was responsible for the Second Impact and shows him the original Evangelion while introducing him to Gehirn. After Yui’s contact experiment with Eva 00, Gendo changed. He became the commander of the new organisation that took Gehirn’s place, NERV. Gendo was also placed in charge of the Instrumentality Project about this time.
Gendo seems content that Fuyutsuki is safe after his abduction.
He has ordered that Eva 01 be placed on standby, meaning there are only two available Evas to fight the Tenth Angel. During the battle he vetoes Shinji’s idea to use Eva 01 to save Asuka, and instead asks Rei to use the Lance of Longinus to kill the angel. When Fuyutsuki cautions him against using it, Gendo replies that the Committee has already started mass production of the Eva series and needs to move time faster by his own machinations. He is chewed out by SEELE for its use after the battle.
When the Eleventh Angel attacks, he orders that Eva 01 continue to remain in the cage. In it’s place, Eva 02 is sortied with Kaworu as her pilot.
When the contamination of Eva 00 worsens during the Eleventh Angel's attack, he lifts the freeze on Eva 01 so that it can rescue Rei. He is shocked when Rei destroys herself and Eva 00 in order to defeat the angel. After she is revealed to be alive SEELE demands answers, so he sends them Ritsuko.
In flashbacks, Ritsuko reveals that he approached her at her mother’s funeral and asked her to support him in the same way as her mother had.
After the Dummy Plug system has been destroyed, he questions Ritsuko of her motives with little success. He talks to Eva 01, again calling it Yui, musing that he will soon be able to meet her. Gendo takes the unfrozen Adam embryo that Kaji brought for him and eats it. When the last angel attacks he is aware SEELE is trying to advance the schedule, but plots to deny them this by attacking with Eva 01.
Gendo feels that SEELE attacked because he has all the cards –Adam, Lilith and Eva. He thinks that even had Kaworu attempted to initiate Third Impact it would have been incomplete, due to the lack of the Lance of Longinus and the most essential part – Lilith’s imperfect heart. He appears to be discussing Rei.
Gendo calls for battle stations after the hacking of the Magi fails. He himself leaves the bridge and is then seen just as Shinji is about to be executed by the invasion forces. He draws the attention from Shinji and is able to deflect the bullets using an AT Field generated by the Adam embryo now in his hand. After saving Shinji he asks him to again pilot the Eva, telling him that not only did he never love him but he was jealous that his son got Yui’s attention. During this scene he reveals he genuinely loved his wife, seeing her as the only hope that God ever gave to him. After she vanished he became a bitter man seeking revenge against God and to become God himself so that he will never lose anything ever again. Feeling that his son shares his sentiments, he asks him to join with him. When Misato arrives to take Shinji to Eva 01, he holds off the troops so that Shinji can help him fulfil his plan. Gendo then makes his way down to the Dummy Plug plant were he finds Rei.
Upon arriving in Terminal Dogma he is met by Ritsuko, and shoots her after her failed attempt to destroy them both. He tells her that he did love her.