Unlock the following bonuses by completing the corresponding party member's Loyalty missions. You will also unlock their individuals skills for Shepard, alternate costumes, and increase the chance for surviving the suicide mission. Note: Complete the Advanced Training research upgrade for your ship to be able to select the skills:
Armor Piercing Ammo
Archangel's Loyalty mission.
Jacob's Loyalty mission.
Kill Samara during her Loyalty mission and have Morinth replace her.