She is first seen briefly when NERV is given command of the defence against the angel, and appears again whilst Shinji is being inserted into Evangelion Unit 01 to attack the Third Angel. She appears shocked when Eva 01 receives damage soon after. Maya is stunned when the Third Angel self-destructs.
She reappears in Volume 2, operating on the bridge during the fight with the Fourth Angel.
Maya was involved in the Eva 00 activation test where Rei was injured and Commander Ikari burnt his hands. She was also present at the reactivation test, alongside Ritsuko and Commander Ikari. When Misato was compiling data on the Fifth Angel, Maya was with Ritsuko in the cage examining the damage to Eva 01. She is later seen at Mt Futago for Operation Yashima. It is Maya who realises that the angel is again using it’s particle beam weapon, which sabotages Shinji’s first shot.
She reappears at the bridge during the second confrontation with the Seventh Angel.
During Rei’s synchronisation test with Unit 01, Maya is seen alongside Ritsuko monitoring her progress. They seem to be working on a dummy system, but Maya has her doubts regarding it’s nature. Maya is also present on the bridge when the angel appears in orbit. Afterwards, she is told by Ritsuko to reroute all power to the Magi supercomputers and Central Dogma.
After the power is restored, she is with Ritsuko explaining to Misato the blackout and how the recovery process went.
Maya is present at the meeting regarding the destruction of the Nevada Branch, listing possible causes for it’s disappearance. She later finds herself a victim of Kaji’s flirting. After Matsushiro explodes during Eva 03’s start-up experiment, Maya calls Shinji and tells him to get Rei and Asuka to headquarters immediately. During the battle she is ordered to switch Eva 01’s control to the Dummy Plug, and despite initial doubt she does so. During the fight between the Dummy Plug and the angel, she throws up.
She is sending commands to Eva 01 in an attempt to force-eject Shinji, but the Eva is ignoring the commands. Maya later tries to operate the Dummy Plug during the battle with the Ninth Angel, but Eva 01 refuses to accept it. Later she is disheartened when Eva 01 runs out of power, mentioning that the Eva was their only hope. She runs out onto the GeoFront with Ritsuko, Misato, Aoba and Hyuga. Maya is the one to realise that Shinji has a 400% synch ratio. Like in the battle against Eva 03, Maya throws up when the battle becomes too much for her.
After the battle, Maya is grateful that the Magi systems are transplantable, making it easier to resume work. She doesn’t like Ritsuko’s suggestion of working in the secondary command centre, citing the lack of comfort and the stiff sensors. She is involved in trying to force-eject Shinji’s entry plug soon after. With Ritsuko she manages to come up with a plan to save Shinji from within the Eva.
Along with her colleagues, Maya is involved in the salvage operation to rescue Shinji. She realises that he is rejecting the signal and choosing to remain in the Eva.
Maya is seen with Ritsuko monitoring Asuka’s synch test, and wonders what’s eating at her. Later, she is seen at Ritsuko’s side when the next angel attacks. When Asuka defies orders and attacks the angel herself, she is asked to speed up the rewriting process for Eva 02’s core. During a test with Kaworu before the core is rewritten, he stuns her by synchronising with it perfectly. She realises that it’s technically impossible, but acknowledges that the Magi computers don’t detect an anomaly. She is later present during the battle with the Eleventh Angel.
When Rei self-destructs Eva 00 to defeat the angel, she is shocked. When Misato asks for the status of Eva 00, she is crying when she tells her that there is no confirmation of the entry plug having been ejected.
Hyuga reveals that he stole some information from her files, discovering that Kaworu could set his synch ratio at will. Maya is present on the bridge during the final angel’s attack. After Kaworu is killed as the final angel, she is confused that access to and from the headquarters has been restricted. She is on the bridge later attempting to defend the Magi from a hacking attack, and expresses her shock at learning that NERV will be forced to attack human invasion forces.
Maya is horrified when Aoba hands her a gun to defend herself, claiming she couldn’t shoot at a human being. She appears more in her element after Eva 02 is reactivated, helping to coordinate Asuka’s attacks from the bridge.
After realising that the MP Eva’s have been defeated, she orders Shinji to get Asuka somewhere safe. She is horrified when the Eva’s arise, still not quite dead.