Shinji pursues Ren after he loses his memory while Yui returns to her brother's university in an attempt to locate his whereabouts. In the meantime, Reiko is investigating the mysterious disappearances of several passengers on a train.

Ren's past comes to light as both he and Yui return to Shiro's last known whereabouts and the birthplace of Kamen Rider Knight, as well as Eri's fate following the secret experiment's aftermath. When Yui finds nearly dead Professor Ejima in the Room 401, he blames Yui for causing a disaster before he dies.