After going underground to talk with Iza, he revealed he built the E5 MkII knowing Kairen's intentions. Following the dissipation of Kitoralsus threats, the E5 MkII remains on standby, Hayato having resigned as driver.
The exterior design of the E5 is broadly based on the experimental Fastech 360S train, with a colour scheme of "Tokiwa" (常盤) green for the upper body and "Hiun" (飛雲) white for the lower body, separated by a "Hayate" pink stripe.
The E5, when transformed, becomes a humanoid mech, which still keeps it's chest the same the nose of it's shinkansen mode and has access to the Turnstile Blade, a large katana which can trap enemies in an energy cage similar to a station gate from a modern era train station. The E5 MkII is also faster and stronger than the original, being able to deal damage to Kairen while the others barely scratched him. Unlike the original, the E5 MkII is a 3 car formation, and can operate without Shashot if required (something the original only did during it's final trip underground). The Turnstile Blade is also stored in a sheath known as the Blade Case, which is required for the energy cage. Additionally, it lack wings, and has more hints of gold. The E5 MkII is also taller than a 2 car Shinkalion, and unlike the original, has twin barrels instead of one for the Dual Gran Cross. The E5 MkII also has an new combination function, whick works with any 2 car shinkalion.
- Though the E5 MkII replaces it's predecessor as the flagship shinkalion, the original E5 still appears though other means.