Fallout 4 The Institute side quests become available if you choose to join this faction and support Father. In Fallout 4, during these side quests there will be moments when you can change your loyalty to the Brotherhood of Steel.
Fallout 4 The Institute Faction Quests
Changing your loyalty will trigger a different set of side quests. However, if you choose to be loyal to Father, the following side quests will be available to you.
Objective: Go to Courser, obtain Rogue Synth, report to father
Your goal is to get the Rogue Synth. To trigger the quest, go speak with Father. Head to the location of the Synth and get back to father afterwards once you’re done. Visit your quarters.
The Battle of Bunker Hill
Objective: Reach Bunker Hill, search for the escaped synths and deal with them.
Speak with Father to trigger this quest for The Institute. Some Synths have escaped the facility and ran away to Bunker Hill. Find and deal with them as Father wishes. Once you’re done, visit the CIT ruins to speak with Father.
Objective: Be present for directorate meeting, talk to Father.
You will have to visit the conference room in The Institute and debate with division heads. Agree to keep supporting this faction and return to Father.
Objective: Relay to Mass Fusion, search for Beryllium Agitator, reach the reactor level after getting the keycard, unlock the reactor and get the Beryllium Agitator, remove reactor level security and exit the Mass Fusion.
Speak with Allie Fillmore to start the quest. Fillmore wants you to retrieve the Beryllium Agitator from Mass Fusion. From here on, you have two options. You can relay to the Mass Fusion and continue supporting this faction to leave the area and inform the Brotherhood to switch your loyalty.
If you choose to keep supporting The Institute, you will be relayed to the Mss Fusion skyscraper roof.
Objective: Talk to Father and reach the house, talk to Minutemen contact, deal with the opposition, speak with Enrico Thompson and Wallace.
This side quest becomes available due to your success in “Mass Fusion.”
Plans to power the Institute reactor are facing some issues due to Wallace, who’s yet to arrive at the facility. Go to Graygardens and look for the homestead west of the hydroponic garden.
Inside, speak with Enrico Thompson. You will find Wallace behind a barricaded door.
Objective: Record the speech, reprogram the transmitter, activate the reactor, attend directorate meeting.
Speak with Father once the reactor is turned on. You will have to record the speech in his quarters.
Now teleport to the Diamond City Market and modify the radio with parts found in the crate. Once you have successfully increased the transmitter’s power, head back to The Institute and from there, visit Institute Advanced Systems
Find the door to the reactor and start it up and once it starts, a directorate meeting will begin.
End of the Line
Objective: Kill Desdemona and Railroad leaders.
Speak with Father to trigger the quest and go kill Desdemona. You also need to eliminate Railroad leaders, relay to the North End Neighborhood of Boston and search for the Old North Church.
Follow the onscreen objectives to complete the quest and kill the leaders once they are gathered in one place.
Objective: Relay to the airport, infiltrate the terminal, deal with Brotherhood Generators, go to Liberty Prime, defend the Synth hacking Liberty Prime.
Go talk to Doctor Li at the Institute Advanced Systems, and say “it’s time.” Now listen to the plan explained by Doctor Rosalind Orman. Relay to the Boston Airport and infiltrate the terminal.
There are three generators in the area you need to destroy. A Synth is at Liberty Prime, go and defend it.
Objective: Talk to Father.
Go tell Father about the safety of Commonwealth at The Institute.
If you have any questions relating to Fallout 4 The Institute faction quests, feel free to ask in the comments.