The Institute is on the verge of a great breakthrough, and if you’re willing to overlook their cruel methods, you can join the scientific enclave and reap the rewards this faction offers. This faction can’t be joined until late in the main story — see what it takes to fight for progress.

An incredibly secretive organization, the Institute are behind the scourge of killer Synths that have invaded the populous of the Commonwealth. Their robotic agents are impossible to identify and completely loyal, willing to kill if compelled by their shadowy masters. You too can take part in the grand experiment with our full faction walkthrough.

See how to get started right with the Fallout 4 survival guide, or get tips to develop 100% happiness settlements.

THE INSTITUTE – Complete Faction Guide

Introduction

The Institute is a faction lead by Father that operates from a location also known as “The Institute’. Members of this group devote their lives to science and to the advancement of scientific understanding, regardless of what it costs. As such, the Institute has a reputation for conducting unnatural experiments on living people and for ignoring whatever basic moral or ethical codes still exist so that new discoveries can be made.

Custom Item – Liam’s Glasses

As a member of this faction, you will have the opportunity to acquire Liam’s Glasses. This item will be given to you by Liam himself as thanks for framing Justin Ayo at the end of the Plugging a Leak quest. The glasses increase Intelligence by 2 points and decrease Charisma by 1 point.

Quest: Plugging a Leak

In order to access this quest, you’ll need to finish the Mankind Redefined mission and ignore the Railroad faction quest called Tradecraft until all of the Plugging a Leak objectives have been completed.

After speaking with Dr. Ayo about the traitor in your midst, follow the waypoint marker to speak with Alan in the Robotics Lab about the Synth escapes and access the terminals on the wall to read the logs until you are prompted to investigate Binet’s quarters.

Travel to Binet’s personal living space to interact with his family before reading the logs found on the indicated terminal nearby and return to the Synth Retention Bureau to access the logs on their computers, then follow the next objective marker to pass through the sliding doors that lead into the Maintenance and confront Eve at the back of the room to have her pull a gun on you.

Depending on how you handle this conversation, the quest can now result in one of two ways.

Method #1: Report Liam as Guilty

Select your lines of dialogue in this order during the conversation with Eve: You’re the Culprit?; Who’s Behind This?; You’d Risk Your Life?.

Activate V.A.T.S. as soon as possible to eliminate Eve with a barrage of critical hits and return to the Binet residence to speak with Liam, then choose “Turn Liam In” from the available dialogue options and report back to Justin Ayo to complete this quest.

Method #2: Report Dr. Ayo As Guilty

Select your lines of dialogue in this order during the conversation with Eve: Drop the Gun; Protecting Someone; Keep the Secret.

Return to the Binet residence to speak with Liam and choose “Ask for Reward” from the available dialogue options before finally agreeing to frame Jason, then access the terminal in Dr. Ayo’s room to disable the safeguards on it and have one last conversation with Liam to acquire Liam’s Glasses.

Joining the Institute

Quest: Synth Retention

After talking to Father and traveling to Nahant Wharf, interact with the Courser to possibly activate or join a battle against an invading enemy force that approaches from all sides and take cover inside the nearest building to start scoring head shots by firing a scoped weapon through the open doorway.

Ascend to the rooftop area to pick off enemies below or in the distance with a scoped weapon or equip something highly-effective at close-range and transfer between the tin shacks that occupy the wharf to clear the rooms inside before sprinting into the next one.

You can also stick by the Courser to eliminate the oncoming threats as a team until the area is clear and another conversation with X6 can be initiated, then ask him for intel on the Synth and select “Let’s Go” to begin the attack on the flotilla.

Approach the south side of the docks to look out across the water at the line of sunken ships curving away towards the left and equip a sniper rifle to zoom in on the area between the first few vessels ahead, then pick off the enemies on the docks and the one that occupies the boat on the right.

Proceed forward towards the flotilla by using your sniper rifle to scout the area ahead and remain close to the Courser to work as a team whenever possible, then make your way across the decks of the interconnected boats to travel east until you reach the trash barge at the end of the line.

Watch for the wooden basket the glides along the rope hanging above to see where box comes to a stop and climb the steps beneath it to step inside, then press the nearby button to start the ride and equip a long-range weapon to target Raiders on the upturned ship ahead.

Use V.A.T.S. to score critical hits against Raiders waiting on the other side of the rope line and duck down within the bucket as you get closer to the opposite ship to avoid taking unnecessary damage, then exit the basket when it comes to a stop and immediately open fire on hostiles occupying the area ahead.

Climb the stairs on the left to clear the next floor above with a close-range weapon and ascend another staircase located at the opposite corner to explore the series of rooms at the top, then approach the furthest back right corner to utilize a third set of steps and open the indicated door to enter the Captain’s cabin.

Search the cabin to refill or acquire any necessary supplies before approaching the ladder and open the hatch above to speak with Gabriel at the top of the ship, then choose You’ve Got Plunder? and You Have My Word as your next lines of dialogue to obtain the Libertalia Password.

Once the conversation has ended, immediately equip a close-range weapon to eliminate the nearby Raiders by sprinting straight into them while firing and activate V.A.T.S. whenever possible to remove threats at a greater speed.

Finish clearing the deck to reclaim the Rogue Synth and report back to Father at the Institute to become a member of this faction, visit your new quarters to speak with the Courser and complete this quest.

Main Quests

Quest: The Battle of Bunker Hill

After speaking with Father and rendezvousing with the Courser at the marked location, travel north to join the Synth on the steps of Bunker Hill and move to the rear end of the bus beside you to jump onto the roof.

Walk forward across the roof of the bus to drop into the territory at the end and equip a close-range weapon to start blasting every Railroad Agent that comes within range, then fight your way over to the current objective marker to open the Utility Basement’s hatch and navigate the tunnel system ahead to reach a landing that overlooks a battle in progress.

Use a scoped weapon or grenades to attack the opposing forces below from a safe distance and descend the stairs to eliminate the remaining few by rushing towards the enemies with a close-range weapon when they’re not looking.

Take out the turrets on either side of the sandbags above with a well-placed grenade toss and enter the room at the northern wall to access the next corridor, then eliminate the Machine-gun Turret MK 1 at the top of the stairs by hitting it head on with a close-range weapon before immediately backing up and taking cover at the halfway point of the previous set of the steps.

Wait for the Turret to approach the top of the staircase without allowing yourself to get caught in its sights and sprint up the steps until you have a clear shot at some small piece of this enemy, then blast it at close range before making another quick retreat into the cover behind you and repeat this tactic until the machine is finally destroyed.

Follow the next catwalk around to destroy the turret in the corner with the help of grenades and fight past another wave of Railroad agents to locate the Escaped Synth in the room at the bottom of the next staircase, then make your next choice carefully as it will effect your relationship with the Institute.

Method #1: Capture the Synth

Approach the Synth escapees to activate their Reset Codes and use this method on each one of them until the entire group has been put into an unconscious state, then exit the basement to report back to Father on the roof of CIT and finish the conversation to complete this quest.

Method #2: Release / Kill the Synth

Approach Y9-15 to tell him he’s Free to Go and open fire on X4-18 at close-range after the cutscene to kill him before causes too much trouble, then approach each of the Escaped Synths to grant them their freedom and report back to Father in the CIT ruins to complete the quest.

You will get the same results by shooting all of the escapees in the head before issuing them any orders at all.

Zoom in with the scope to clear the Synth-occupied balconies that pass in front of you during elevator’s continued descent and push yourself against the left side wall to remain in whatever cover is possible until the car finally stops, then clear the immediate area with a close-range weapon before entering the room to right of the lift.

Ascend to the floor above to reach the corridor on the opposite side of the room and open the Circuit Breaker Lid located on the wall beside the last open doorway on the left, then flip the switch before returning to the elevator and use your card to continue the car’s previously-interrupted descent.

Remain undetected inside the elevator car after it comes to a stop on the floor below and use V.A.T.S. to reveal locations of enemies in the surrounding area ahead, then scan for laser turrets on the ceiling by employing the same method and unleash your first string of critical hits on members of the Brotherhood.

Use the elevator walls as cover while shooting at the laser turrets on ceiling until they explode and finish clearing the area to enter the elevator located in the back left corner of this room, then ride it down to the Reactor Level to descend the stairs on your right and approach the large glass windows ahead to enter the narrow chamber beside them.

Press the button inside to decontaminate before proceeding through the door that opens ahead and ascend to the top of the metal ramp way to press the Interlock Release switch, then remove the Beryllium Agitator that is now available to set off the alarms and then turn towards the south wall with a scoped-weapon equipped to destroy the laser turrets located near the ceiling.

Exit back through the decontamination chamber to encounter a Sentry Bot and use explosive ammunition or grenades in combination with critical hits scored via the use of V.A.T.S. to defeat this enemy, then return to the elevator to reach the previous floor above and open the first door on the left to clear the lobby of all remaining Synths before finally exiting the building.

Report back to Allie Fillmore to complete this quest.

Finish clearing the area to enter the farmhouse and open the Graygarden Homestead door on the second floor to speak with Enrico Thomas in the next room below, then interact with Wallace at the indicated location by asking him to relax before using a threat to progress the conversation and continue using persuasive dialogue until he accepts your offer to complete this quest.

Enter the broadcasting shack to locate the Radio Parts Crate under the red desktop and collect the pieces inside to approach the white bin with a toaster on top of it, then choose the Thing With Tubes to repair the machine and step over to the middle control panel with circular gauges on it to insert the Radio Thing With Buttons.

Face the next control panel on the right to use the Thing With Dials and report back to Father at the Institute to receive his next set of instructions, then open the indicated Reactor Door to activate the core inside and exit the chamber to approach the closest available terminal.

Use the terminal to check the statuses and initiate the startup sequence to activate the reactor, then speak with Father again before exiting the area to return to Advanced Systems and follow the current waypoint marker to locate the meeting room.

Sit down at the head of the table to start the meeting and exchange words with the rest of the board to learn about their plans, then make a decision between focusing resources on weapons or focusing resources on Synths to bring this discussion to a close and complete the quest.

Approach Desdemona to tell her you want to help the railroad and back up towards the entrance as Railroad agents begin filing into the room from all sides, then select a molotov cocktail (or grenade if that’s all you have) and toss it directly into the group of people that currently surround the on-screen objective marker.

Use the columns near the Railroad HQ’s entrance as cover to remain at somewhat of a distance from the enemies ahead and continue tossing flaming or exploding projectiles towards the current objective markers to eliminate the leaders of this faction, then equip an automatic weapon to consistently hit your targets without having to rely on accuracy and finish clearing the room before reporting back to Father to complete this quest.

Head towards the current objective marker by taking out enemies in the distance ahead with a scoped-rifle while V.A.T.S. is activated and continue clearing threats from the path in front of you to eventually infiltrate the Terminal, then secure the room by sprinting up to each available guard in the area and eliminate them quickly with several blasts from a close-range weapon.

Proceed to the east end of the building to climb the steps in the corner that lead onto the roof and score a series of critical hits on the surrounding enemies at the top to eliminate them quickly, then cross to the opposite side of the launchpad to destroy the indicated Generator and turn back towards the Terminal to enter the glass corridor on the left.

Use V.A.T.S. to take out the Knight with his back turned at the end of the hall and enter the next elevator ahead to descend into the control tower below, then equip a close-range weapon to eliminate the automated security on your left and destroy the second Generator around the corner before returning to the rooftop above.

Exit the glass corridor to approach the remaining objective marker on your left and defeat the patrolling Knights by scoring critical headshots from a safe distance, then destroy the third Generator to receive a new waypoint and follow it to discover Proctor Ingram’s location within a circular metal structure that looms above you.

Score a critical headshot on Proctor Ingram to knock him off the walkway above and climb the staircase on your left to reach Liberty Prime’s head at the top, then aim a long-range weapon into the courtyard below to pick off various threats with the help of V.A.T.S. and continue defending the area until the Synth finishes hacking to complete this quest.

Side Quests

Quest: A House Divided

You will need to complete the Mankind Redefined mission to access this mission.

After speaking with Newton Oberly in the Bioscience sector of the Institute, proceed through the sliding doors he opens to reach another set of doors at the end of the next corridor and equip a scoped-rifle to eliminate the enemies waiting on the other side by scoring headshots while walking backwards.

Open the sliding doors on the east wall of the room that was just cleared to peer out into the adjacent hallway and destroy the ceiling turret on the left with a scoped-weapon to remain unscathed while attempting to unlock the room directly across from you.

Collect the supplies inside the small room before proceeding towards the current objective marker and open the next two pairs of sliding doors directly ahead to reach a third one that’s located by a microscope on a table, then pick the lock to access the Fev Lab and make your first available right to open the door at the end of the corridor.

Enter the BioScience Observation Room to approach Lawrence and decide if you want to end his protest peacefully or if you want it to end in violence.

Method #1: Peacefully

Start a conversation with Lawrence to use these lines of dialogue in the following sequence: Talk About This?; Give Me a Chance; Is That What’s Best?; Give Me a Chance.

After Lawrence exits the room, report back to Newton to complete this quest.

Method #2. Violently

Use the terminal next to the window to deactivate the turrets and release Synth Gorillas into the room where the protest is currently being held, then stand back to watch as the monsters on the other side of the glass maul the scientists until they’re dead and report back to Newton afterwards to complete this quest.

Follow Roger along the shoreline to speak with him again so that you can hand over the Modified Seeds and finish the conversation you’re having about Bill Sutton to receive a new objective, then return to the garden to interact with Janey and select the Trying to Help option to discover Bill’s plans.

Travel to Goodneighbors to make your way towards the current objective marker and open the indicated door to enter the Third Rail, then find Cedric Hopton sitting at the bar to ask him about Bill’s plans and select a Sympathetic approach to finish the conversation.

Exit the Third Rail to return to the Warwick Homestead and enter the house to confront an armed Bill Sutton inside, then select the dialogue options in this order: Sure About This?; And the Children?; Yes.

After Bill exits the house, speak with Roger and report back to Isaac Karlin to complete this quest.

Rule the Future – Fallout 4 Institute Faction & Ending Guide

Table of Contents

Table of Contents

THE INSTITUTE – Complete Faction Guide

Introduction

Quest: Plugging a Leak

Table of Contents

Joining the Institute

Quest: Synth Retention

Table of Contents

Main Quests

Quest: The Battle of Bunker Hill

Table of Contents

Quest: Mass Fusion

Table of Contents

Quest: Pinned

Table of Contents

Quest: Powering Up

Table of Contents

Quest: End of the Line

Table of Contents

Quest: Airship Down

Table of Contents

Side Quests

Quest: A House Divided

Table of Contents

Quest: Building a Better Crop

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