In the comics, they explained that his partner lost consciousness during the Kaiju fight seen in the flashback/Mori's dive in the first film.
Also in the comics, him and his partner were discharged because she got terminal cancer from piloting Coyote Tango, a Mark-1. The cancer may have been the reason for loss of consciousness and thus they didn't want to risk a copilot suffering the mental overload.
Pentacost also contracted terminal cancer after his discharge.