You need to do all there loyalty missions and research the thanix cannon multi-core shielding and silaris armor upgrades for the normandy. If you want the npc crew of the normandy like kelly and the engineers to survive as well you need to leave on the suicide mission right after the ship is attacked by the collectors. Sometimes some of your squad will still die but i believe this is only because you havent gotten all there conversations. If this happens just restart and put the person who died in your actual party when you fight the reaper. Samara is a good biotic barrier for the seeker swarms. I used zaeed to escort the civis miranda to lead the first fire team and garrus to lead the second. I used legion for the whole going through the vent shaft thing.
Mordin died but i just restarted and put him in my party. Then everyone lived.