Four years have passed since Third Impact. Society has rebuilt itself rather well; thanks to a surge of Spiral Energy from EVA-01's wings, hundreds of thousands of AT-Fields have reconstructed themselves through sheer willpower. Shinji, though no longer absolutely insane, is now a cynical, self-loathing loner who does not want to face the remains of the society he destroyed.
Then, a fleet of strange face-covered spaceships suddenly appears, and bombs down much of Earth and the LCL ocean. In all the confusion, Shinji encounters a face-shaped meteorite, which has a cockpit. Wary of mecha ever since his time as an EVA pilot, he considers leaving the Mini-Mecha - until his cross-shaped necklace turns into a golden drill pulsing red light.
Shinji changes his mind, approaching the mecha and controlling it with his Core Drill. As he navigates the mech throughout the remains of the city, he finds a relatively large group of survivors, led by a young idealist scientist and his younger sister who take an interest in Shinji's mech. Shinji offers to give it away, but the mech will only work if Shinji himself pilots it. Reluctantly, Shinji accepts the mech, and teams up with the scientist to reverse-engineer mecha called Ganmen from Shinji's mech, which has been codenamed "Headmaster".
Months or years pass. Shinji is skilled in the Headmaster unit's controls, somewhat glad that, unlike an EVA, the Headmaster does not automatically take over. He and the scientist make a good tag team; with the scientist in his personal Ganmen, the Kuro Rex, he can throw Shinji and take out targets from a distance. Shinji is also beginning to learn to warm up to others, though he is still conflicted about his role after Third Impact.
Then the first wave of Mugann attacks. None of the conventional weaponry of the Ganmen can stop them, and many lives are lost. Shinji's drill catches and returns one of the Mugann beams, but collateral damage is heavy. Suddenly, a voice tells Shinji to drill on the top of the Kuro Rex; despite the absurdity of the idea, the scientist agrees, and the two combine. The Kuro Rex gains drill powers, and finishes off most of the Mugann with ease. Unfortunately, the anti-whiplash function of the Kuro Rex malfunctions, it takes a Mugann beam from the side, and the scientist's neck is snapped in the collision. Shinji flies into a rage, and swiftly and fiercely destroys the rest of the Mugann.
After the scientist's burial, Shinji refuses the sister's attempts to pilot in her brother's stead, saying she already has a Ganmen, and he can pilot it alone; she reluctantly agrees. Shinji requests some modifications to the Kuro Rex, to make it more aesthetically pleasing. Though the rebuilt mecha unwittingly has an uncanny resemblance to EVA-01, Shinji does not wish to reject the design; in fact, he likes it, because it reminds him of his mother's spirit. He opts to rename it from "Kuro Rex" to "Lazengann", now that the Headmaster has been inserted and the mech is now his. He resolves to fight, to not be responsible for the apocalypse again; he says he wants to be "an eternal testament to the existence of Mankind".