Rebuild of Evangelion
Shinji in Rebuild of Evangelion, while mostly the same as his anime counterpart, comes across as somewhat more angry about his situation (although he isn't outwardly angry like his manga counterpart with Sadamoto's take on the series). For instance, he calls out Misato and other members of NERV as being selfish and bemoans the fact that he's "left feeling scared" when he and Rei have to pilot during the Operation Yashima battle. Somewhat similar to his feelings in The End of Evangelion, Shinji realizes that he "has no freedom" and "has no choice but to pilot Eva" when he attempts to run away from NERV after the Fifth Angel battle. Although he decides to stay in Tokyo-3 instead of leaving like in Episode 04 of the series, Shinji can't help but feel that he's only needed for piloting Eva and that nobody truly cares for him.
These feelings are dissolved to an extent when Misato shows Shinji the Angel identified as Lilith in Terminal Dogma, explaining to him why he and the rest of NERV have to do what they can to prevent Third Impact from happening. He agrees to pilot Evangelion Unit-01 once more, and together with Rei Ayanami in Evangelion Unit-00, the Sixth Angel is eventually defeated during the Operation Yashima battle.
Shinji's relationships with the other characters in Evangelion: 1.0 You Are (Not) Alone are similar to those in the series. A difference with his relationships towards Misato Katsuragi and Rei Ayanami, however, is that he is somewhat physically close to them as the film progresses. When Misato shows Shinji Lilith, Shinji lets Misato hold his hand. Also, when Shinji checks on Rei in her entry plug after the Sixth Angel's defeat, the two hold hands as Rei smiles at him.
As the story advances into Evangelion: 2.0 You Can (Not) Advance, Shinji is somewhat more accustomed to living in Tokyo-3. His friendship with Toji and Kensuke is a solid one (due to them becoming friends in the first film) and he has occasional conversations (as well as smiling around) Rei. Shinji also becomes friends (and additionally roommates) with Asuka, but so far shows no romantic interest in either pilot. Shinji briefly meets Mari Illustrious Makinami twice during the film, but he knows nothing of her, save for a few verbal exchanges. During lunch with his friends at a marine preservation institute, Shinji mentions that he learned to cook meals because Misato didn't know how to. He makes lunches for Misato, Asuka, as well as Rei during the film. Shinji hopes to get along with his father and is happy when Gendo complements him after the Eighth Angel attack. Shinji is unaware that Rei tried to surprise him by inviting Gendo to a dinner party. The plans for the party were cut short, however, by the Ninth Angel's attack.
After Shinji's inability to fight the Ninth Angel-possessed Unit-03 which carried Asuka, Gendo orders the activation of the Dummy System, which tears the Eva to pieces, unintentionally injures Asuka and enrages Shinji. He attempts to destroy NERV headquarters, but Gendo orders to cut him off from the Eva, causing Shinji to faint. Shinji has a flashback of his younger self. When he awakes, he is brought to Gendo, telling him he'll never pilot again, and leaves NERV. Misato attempts to comfort him but fails. Gendo orders the erasure of his records, intending to replace him with the Dummy System. During the Tenth Angel's atack, Shinji unexpectedly encounters Mari, who tries to convince him to pilot. Much determined, Shinji urges Gendo to let him pilot again, and he attempts to rescue Rei, who has been absorbed by the Angel. Shinji thanks Rei for her efforts of bringing him and his father together. Rei apologizes that she couldn't do anything, but Shinji says it's okay. Shinji's decision to save Rei unintentionally awakens Unit-01's pseudo-evolution and causes Near Third Impact, only to be halted by Kaworu's intervention, spearing Unit-01's core.
By the start of Evangelion 3.0, fourteen years have passed since Near Third Impact. Shinji has spent that time inside the core of Unit-01, which was sealed inside a Tesseract orbiting Earth. After Asuka retrieves Unit-01, Shinji is salvaged from its core and is welcomed with rejection by Asuka, Misato, and the crew of Misato's ship, the AAA Wunder. Shinji is fitted with a DSS Choker to his neck that will kill him if he attempts to pilot an Evangelion again; he learns that Misato and the Wunder's crew now belong to an organization called WILLE, which is devoted to destroying NERV and its Evas. Shinji questions his rejection when Evangelion Mark.09, seemingly piloted by Rei, attacks the Wunder and retrieves him. Misato contemplates activating the choker, but holds off until Shinji is out of range.
Shinji is taken to the ruins of NERV Headquarters. He finally meets Rei, relieved to have saved her. She takes him to Gendo, who tells him he'll pilot Evangelion 13 with Kaworu. He then meets and befriends Kaworu, who fixes his broken SDAT player and teaches him to perform a piano duet. He also tries bringing books to Rei. Answering Shinji's questions about why people are hostile to him, Kaworu shows him the ruins of Tokyo-3 and explains how his awakening of Unit-01 was "the catalyst" for Near Third Impact and further ravaged the world and its remaining human population. Shinji replies he only wanted to save Rei, but Kaworu tells him humanity does not see it that way. Shinji also meets Fuyutsuki, who reveals that he didn't save Rei after all and that "Rei Q," who rescued him, belongs to a series of clones of his mother, who exists within Unit-01 as its "control system." Realizing his failure, Shinji suffers from a nervous breakdown after he realizes that his efforts are totally useless. With Kaworu's encouragement, Shinji agrees to Gendo's plan of reversing the Near Third Impact by piloting Evangelion 13 with Kaworu and removing the Spears of Longinus and Cassius from Lilith's corpse inside Terminal Dogma. Before the mission, Kaworu removes the choker from Shinji and places it on himself as a sign of trust.
Shinji and Kaworu arrive in Terminal Dogma, escorted by Rei Q inside Mark.09. Kaworu expresses reluctance to remove the Spears after noticing they are an unusual shape, but Shinji is seemingly determined to continue. They are attacked by Asuka and Mari, who have followed them into Terminal Dogma. Shinji initially refuses to attack Asuka, and says he wants to save the world by pulling the Spears, but Asuka is flabbergast, and asks him if he is trying to start another Impact. He eventually strikes back, to Asuka's outrage. Despite their efforts and Asuka and Kaworu's pleas, Shinji uses Evangelion 13 to successfully remove the Spears. However, doing so releases the Twelfth Angel from Evangelion Mark.06, which is eaten by Evangelion 13 and triggers the Eva's awakening. Evangelion 13 flies out of Terminal Dogma and begins Fourth Impact. Witnessing Fourth Impact, Shinji starts to regret pulling out the Spears. As Evangelion 13 and Mark.09 battle with the Wunder, Kaworu tries to stop Fourth Impact by allowing the choker to detonate and kill him. The Fourth Impact is only stopped after Shinji's entry plug is forcibly ejected from Evangelion 13. Afterwards, a catatonic Shinji is found inside by Asuka, who drags him out and derides him as a "brat", criticizing Shinji for always running away from his problems. Upon meeting Rei Q, the three walk through a red desert to where Asuka says "the Lilin are."