Evangelion: 3.0+1.0 Thrice Upon a Time

In the heart of Paris, a dedicated team from the WILLE organization, led by Maya Ibuki, embarks on restoring the city and its defenses. Their labor is interrupted by an unexpected assault from NERV forces, but their efforts are met with the protection of the Wunder fleet.

During the attack from NERV, Makinami Mari Illustrious pilots Unit-08 and valiantly fights back against the invaders. Her successful defense allows WILLE to continue their important work in restoring Paris.

Meanwhile, Shinji Ikari, Asuka Langley Shikinami, and Rei Ayanami find themselves in the outskirts of Tokyo-3. They stumble upon a settlement filled with survivors, where they reconnect with their childhood friends, Toji, Hikari, and Kensuke, who have all matured and found new paths in life.

In the settlement, Shinji meets Toji, now a doctor, Hikari, who is a mother, and Kensuke, who has become a technician. The emotional reunion underscores Shinji's journey towards healing from his past traumas.

As Shinji begins to overcome his emotional scars, Rei finds contentment as a farmer in the community. However, her vulnerability from lacking LCL fluid leads to a poignant farewell with Shinji, marking a bittersweet moment in their friendship.

The Wunder arrives to collect Shinji and Asuka. However, upon their arrival, Shinji feels isolated and disconnected from his past, hinting at the personal conflicts that lie ahead.

Before embarking on their next mission, Asuka and Shinji engage in a heartfelt reconciliation. Asuka confesses her long-held feelings for Shinji, and he expresses regret over his past indecisiveness, particularly regarding her near-fatal clash with the Ninth Angel fourteen years earlier.

As the Wunder sets out, it is ambushed by a fleet of NERV ships and a swarm of EVA units. In the ensuing combat, Asuka and Mari team up to protect their vessel from incoming threats, attempting to thwart the revival of Unit-13.

In a tense moment, Asuka discovers Unit-02's resistance to her commands, leading her to remove her eyepatch. This act reveals her connection with the Ninth Angel, forcing her to confront her own identity as she transforms her EVA into an EVA-Angel hybrid.

Inside the NERV vessel holding Wunder captive, Misato Katsuragi confronts Gendo Ikari. During this confrontation, Gendo unveils his transcendent ambitions using the Key of Nebuchadnezzar, revealing the controversial plan for the Human Instrumentality Project aimed at reshaping human existence.

The battle escalates as the Wunder crew faces heavy resistance, leading to a thrilling encounter between Shinji and Gendo within a bizarre 'Anti Universe'. Gendo's dark intentions concerning the 'Black Lilith' and the Additional Impact are laid bare, showcasing the depths of his obsession with his lost love, Yui.

In a critical moment, Misato orchestrates an evacuation for the Wunder crew while sacrificing herself and the ship to create the 'Lance of Gaius'. This act empowers Shinji with the necessary means to reshape reality amidst the ongoing chaos of the battle.

In a profound culmination of events, Shinji finds closure with Gendo and reciprocates Asuka's feelings. He comprehends the cyclical nature of their existence alongside Kaworu and ultimately decides to reset the world, aiming for a future free from the burdens of the past.

As the reset takes effect, Shinji, now liberated from his heavy responsibilities, envisions a flourishing world for humanity. Gendo and Yui willingly sacrifice themselves to facilitate this new beginning, ensuring that all affected beings are restored.

The story concludes with Shinji waiting on a peaceful beach until Mari arrives, signaling the end of her Evangelion. Their romantic connection blossoms as they joyfully embark on a new adventure together, reflecting a hopeful outlook for the future.