THE INSTITUTE QUEST 01 - Synth Retention
Triggered by completing Story 11 - Institutionalized
Objective: Talk to Father
Now that you've explored the Institute and gained access to and from the place, Father wants a word with you. When you arrive, it seems a synth on the surface has gone rogue and is wreaking havoc as the leader of a gang of raiders. Agree to help the Institute and the synth's location will be added to your map and you'll be tasked with meeting up with a nearby courser for this retrieval operation.
Objective: Meet up with the courser
The courser is located on the far East side of the map, so unless you have explored that area already you are likely in for a fair trek. The area is surrounded by water, so you can simply swim there if you have the aquaboy/ girl perk and bypass all enemies along the way. When you eventually reach your destination, you'll find the courser down a short alley. If you have high charisma, you can covince him to hand over some grenades before you begin the assault on the gang.
Objective: Reclaim the rogue synth
A little bit of forewarning here. The gang is housed on a flotilla of rafts and boats leading out to a sunken container ship where the synth can be found. This area is highly open, meaning those who use short range or melee weapons will be at a severe disadvantage. Use long range weapons and sneak attacks to bring down the wandering raiders without alerting the whole lot of them. If you don't have long range weapons, you'll just have to move from cover to cover position as best you can. There are also a lot of safes and other goodies to loot as you move along the lines of ships, so take the time to explore as you go.
Take your time and move carefully along the rickety walkways towards the giant container ship at the back. Eventually you'll reach a point where you can get no closer. You'll see a wire strung from the platform you are on to the container ship. A cable car here can be used to get across. Press the glowing red button to summon the car (or if you are seen by enemies, they will come across on the car themselves). Cross to the container ship and start working your way upwards methodically.
Note: After going up the second set of steps (the fourth floor, just above the water being the first floor), you can move out on a wooden platform with a chair on the end which overlooks the front of the ship. On the table beside it is a copy of a U.S. Covert Operations Manual for you to grab.
Keep going up and you'll enter the captain's cabin. The courser X6 will briefly talk to you here and give you the rogue synth's reset code, which could come in handy when you confront him shortly. Directly in front of you when you enter will be a crate with the legendary combat shotgun Le Fusil Terribles which is a nice little addition to your armoury. Look around in the cabin for a ladder leading up to slam straight into a confrontation with Gabriel the escaped synth when you take it.
Gabriel will talk to you for a bit. You can use the reset code on him during the conversation to remove him from the upcoming (unavoidable, even with persuasion) fight, making the other gang members immediately open fire. Attempting to persuade him will result in the other gang members calling out for him not to listen before they open fire on you. So, you're pretty much going to have to fight your way through. Take what cover you can though as the members who are with Gabriel are often higher level raiders (survivalists) and are much tougher than regular raiders. When the confrontation is over, X6 will teleport Gabriel back to the Institute. There is a red loot crate as well as a safe to raid up here as well. After that, it's time to return to the Institute to report your success.
Objective: Return to Father
Talking to Father will result in a few lines of dialogue and him informing you that you now have a room inside the Institute.
Objective: Visit your quarters
Follow the marker through the winding tubes and corridors to find your own little place. Shortly after you enter, X6-88 will arrive and inform you that Father wants to see you again, finishing this quest and starting The Institute Quest 02 - The Battle of Bunker Hill.