Don't you know people don't use those anymore. duh. lol. But seriously, they really should.

Anyway, (SPOILER)the scene at the beginning of DoC shows Vincent pulling a gun on Hojo slumped at his computer having already uploaded his consciousness, then an explosion distracts Vincent and Hojo disappears.

In FF7, defeating Hojo seemed to prompt him to explode or something. You don't see his carcass lying on the tower, but then again you're not really up there for very long. Hojo must have simply pulled a Houdini until he could carry out his backup initiative.