Jack, Legion and Mordin died.
Legion got carried off by a seeker swarm, because I didn't have a loyal biotic with me during the long walk. I picked Jack because she was supposed to be the strongest biotic in-universe, even though she wasn't loyal.

Mordin and Jack died because I left them behind to guard the door while I dealt with the human Reaper. My critical mistake was in sending Grunt to escort the scientists; a hidden stat governs who survives this part, preferring to kill non-loyal characters first. Jack died because she wasn't loyal, and sending Grunt away brought the average defense total down for Mordin to get killed.
I'm kinda conflicted. I didn't want a perfect playthrough to import into ME 3 because that would be boring and predictable... however, I miss Legion and Mordin. Why couldn't it have been Jacob? Whyyyyyyyyyyyy