Shinji Ikari originates from a parallel world and pilots specialized units called Shinkalion 500 TYPE EVA and Shinkalion Z 500 TYPE EVA. These units differ from other Shinkalions due to their interdimensional origins and design connections to Evangelion technology.

In the first season, he initially appears piloting a black shinkansen train that later transforms into the Shinkalion 500 TYPE EVA. He collaborates with Hayato Hayasugi's primary team to combat Kitoralsus, participating in joint operations where his unit integrates with other Shinkalions during battles.

During the film *The Marvelous Fast ALFA-X That Comes From the Future*, Shinji returns with Rei Ayanami and Asuka Langley Soryu to confront new space-based threats led by Nahane and Ohanefu, endangering Earth. He pilots the Shinkalion 500 TYPE EVA alongside the prototype Shinkalion ALFA-X, driven by a younger Hokuto Hayasugi from the future. Their combined efforts with the Shinkansen Ultra Evolution Institute's drivers neutralize the extraterrestrial invaders.

In *Shinkansen Henkei Robo Shinkalion Z*, Shinji continues as a pilot, now operating the upgraded Shinkalion Z 500 TYPE EVA. He participates in missions against giant mechanical Get beings, utilizing new Zailiners enhancement systems. His collaboration extends to drivers from the second generation of Shinkalion teams, reinforcing his status as a cross-dimensional ally.

Shinji's driver suit resembles an Evangelion plug suit in a simplified design, lacking elements like chest numbering or interface headsets. It incorporates standard Shinkalion equipment such as shoulder pads and headphones. His relationships include brief partnerships with Hayato Hayasugi and interactions with characters like Rei and Asuka during crossover events.