To begin the first of this faction’s quests, you must complete Main Quest: Institutionalized, find Father, and agree to his request. You are free to continue Institute operations for as long as you wish. Please be aware that your relationships with the other main factions—the Brotherhood of Steel, the Railroad, and the Minutemen—may be negatively affected the more Institute quests you complete. It seems you can’t be friends with everybody.
Fallout 4 eGuide DATA The Institute Quests