As you complete the Main Story Missions in the game, you will unlock side quests given to you by your various homies on the ship. These side quests are nothing more than the various activities you could already do in the game, except they are part of actual quests.
Note that you can complete the activities as you're free roaming and when you do the side quest involving them, you won't need to complete them again. You will get rewards for completing these side quests, usually in the form of upgrades to your weapons and powers. Sometimes, you can unlock certain weapons earlier than during the actual story.
