Siding with the institute I wondered why other factions had to be destroyed. The Institute is well known for replacing people with synths. The PC has almost unrestricted access to each of the other factions so they could get dna samples. Maintaining the factions has a lot of utility. Secretly controlling the Railroad allows escaped synths to be recaptured easily or re purposed for other missions and later become secret police to promote acceptance of synths. The BoS provides a high amount of powerful soldiers that can be exhausted fighting mutant and raider strongholds chasing false Institute leads. Re purposing the Pedwyn, new reactor and improved engines, and Liberty Prime, replace nukes with reactor to power personal teleporter and stealth field, when loyalists have been removed gives a great enforcement tool to ensure safety for above ground installations. The minute mend don't get replaced, they are alright, they get upgrades. Gauss mortars with mininukes( regular and MIRV), synth beacons for emergency backup, improved communication systems, and a fancy warehouse to help distributes supplies among settlements (why cant I specialize settlements as mega farms to provide food for industrial settlements).

It would be a series of quests to undermine each faction and replace key personnel. There would be additional missions to supply the Institute with the materials they need. I am sure that a small flying symbiotic parasite could be engineered to make citizens of the Commonwealth and the other factions more accepting of the changes.