It's several days more before Kirk is up, and he really shouldn't be on his feet then either but he is. And when he learns of the empty cryotubes he feels a very real sense of shock setting in.

To him it's not the possibility that they're alive on Earth (if they are he thinks Khan might help him round them up to safety). It's something Khan once said, he made me watch..., something that makes Kirk think they're gone forever. It is something Marcus would do. He wouldn't put anything past Marcus.

He almost has his request to Starfleet finished, but he puts it on hold, and takes his crew to Betazoid. Because they can sense violence from miles away, Kirk is allowed to see Khan alone.