In the Manga

During the final part of the manga Doctor makes both Tōma and Mundock go berserk. Under Doctor's control through nanomachines, Touma tries to attack Eve but Kevin stands in the way and is pierced instead of Eve, and after that they attack Train and River, and eventually Eve takes River's place, and both invent a plan for Eve to destroy the nanomachines that control the two.

In the Anime

e see him face off against the Apostle of the Stars, together with the sweepers from the Alliance. However, none of the sweepers reaches the Apostles' castle, so the scene where both him and Mundock are controlled by Doctor does not take place.

Source: Wikipedia