The End of Evangelion

Shinji Ikari, still distraught over the death of Kaworu Nagisa, pleads for help from an unconscious Asuka Langley Soryu, telling her that he is scared of Rei and Misato and that he needs her. Upset and desperately trying to rouse her from her sleep, Shinji accidentally dislodges her hospital gown and masturbates while standing next to her bed. SEELE, with the Angels eliminated and Gendo Ikari's treachery obvious, attempt to take control of NERV, first by hacking the MAGI computer system (which is thwarted by a firewall installed by Ritsuko Akagi) and then by a large-scale assault by the JSSDF.
The JSSDF soldiers invade NERV's facilities, killing all NERV personnel on sight, with top priority is given to the execution of the Eva pilots and the capture of the Evangelions. Misato Katsuragi orders Asuka to be moved to the cockpit of Unit-02 and placed at the bottom of a nearby lake, and rescues Shinji to have him pilot Unit 01. She is able to bring Shinji to the Eva's bay doors, but is mortally wounded in the process. She persuades Shinji to keep going and pilot the Eva one more time, giving him a kiss, asking him to please come back, and forcing him into the elevator. Before her death, Misato wonders if Kaji believes she has done the right thing.
Concluding that NERV's defeat has become inevitable, Gendo retrieves Rei Ayanami and retreats to Terminal Dogma to begin initiating Third Impact. Meanwhile, Asuka reactivates the sunken Unit 02 upon reaching the epiphany that her mother has "always been with her" within Unit-02. Asuka engages the JSSDF attack force's aircraft and ground vehicles, though the Eva's external power cable is severed during the battle. The "mass-production" EVAs are launched to defeat her. In Terminal Dogma, Ritsuko confronts Gendo and Rei, intending to self-destruct the NERV facility to prevent Gendo from carrying out his plans. However, her command is overridden by Casper, one of the three cores of the MAGI and essentially her mother, and Gendo kills her. At the Eva launch cages, Shinji is unable to enter Unit-01 and join the battle because the Eva is encased in hardened Bakelite. Outside, Asuka initially seems to cripple the new Evas before her internal power is depleted, but the Mass Production EVAs reactivate despite their considerable injuries through their S2 engines and resume destroying the defenseless Unit-02. Back inside the NERV facility, Unit-01 breaks through the surrounding Bakelite on its own. Too late to save Asuka from the EVA series, Shinji sees the mangled remains of Unit-02, Shinji screams in torment.

Inside Terminal Dogma, Gendo attempts to merge with Rei to begin Third Impact. However, Rei takes over the process and reunites with Lilith, the creature crucified within Terminal Dogma, forming a luminescent, rapidly-growing being with Lilith's skin and Rei's body. The Mass Production Evas crucify Unit-01 and begin the ritual to initiate Third Impact, as Shinji is driven to madness. The giant Lilith/Rei being rises out of the Geofront and confronts Shinji, morphing into the form of Kaworu as well as Rei. After several scenes of contemplation, including a surreal and violent confrontation with Asuka, Shinji decides he is alone and unwanted and everyone in the world should die. In response, the giant being creates a planet-wide anti-AT-Field, negating the AT-Fields of humanity and causing their bodies to dissolve into LCL, the blood of Lilith and the primordial soup from which life on Earth originates. The souls of humanity are absorbed into the Egg of Lilith, a giant dark sphere cradled by Lilith/Rei, as she grows to ever-greater proportions.
As the souls form a single, complemented existence, Lilith/Rei again gives control of the process to Shinji. Shinji's emotional sufferings and loneliness prompt him to accept this new form, thinking that there could never be happiness in the real world. After a series of mental journeys and monologues, Shinji realizes that it is necessary to live with others and that to live life is to experience joy as well as pain. The Third Impact is rejected and Lilith/Rei decays and dies, releasing its anti-AT Field and allowing separate beings to potentially come back into existence. Asuka and Shinji are rematerialized from the sea of LCL together on a beach looking out on the severed head of Lilith/Rei and the apocalyptic landscape.