Afterwards, Malcolm finds his way back, and he finds a way to continue on living. Canon-compliant, takes place after the Season 2 finale.
The mission had been simple- simple and boring and virtually impossible to mess up. So of course it had to end in fire, destruction, rebellion, corruption, and Jim Kirk, standing alone in the middle of it all- alone except for a tiny baby girl, representing everything Jim stands for. Gen.
It's Father's Day on the Enterprise, and Jim has been acting strangely. McCoy, as usual, is at his side- and that's exactly what Jim's counting on.