War of the Commonwealth

The War of the Commonwealth is a large conflict that occurs in 2287 between the Institute, the Railroad, the Brotherhood of Steel, and potentially the Commonwealth Minutemen.

Prelude
After years of development, the Institute succeeded in the creation of generation 3 synths, robots completely identical to humans, in the late 2220s. In the years to follow, the Institute began sending these synths out to infiltrate the Commonwealth, whether simply given them false identities or by "replacing" wastelanders with synth copies of them. The existence of these synths became known to the people of the Commonwealth in events such as the "Broken Mask" event in 2229, where a synth began shooting people in Diamond City.

Despite the Institute's belief that synths were no more than tools, it was eventually discovered that synths are capable of both emotion and free will. For this reason, an organization known as the Railroad was founded to help find, rescue, and hide away these synths. The Institute, seeing the Railroad as an annoyance, would launch attacks whenever possible, such as the Railroad Safehouse Raids.

In 2287, a Brotherhood of Steel recon squad detected high energy readings coming from the Institute, prompting Elder Maxson to send the Prydwen to the region, with the main goal of destroying the Institute and its synths, which are seen as abominations of technology. This conflict of goals between the Railroad and Brotherhood also led to conflict between the two factions.

War
The arrival of the Prydwen led to increased hostilities throughout the Commonwealth, including the Brotherhood investigating the C.I.T. ruins and encounters with synths. The Institute also began stepping up efforts to combat the Railroad, such as taking out a route used for smuggling synths out of the region. The Railroad both continued to fight off the Institute while planning on how to deal with the Brotherhood of Steel's arrival.

At one point, the pre-War individual known as the Sole Survivor became involved in the conflict. Searching for their lost son, Shaun, the Sole Survivor confronts and kills Kellogg, the Institute's biggest agent, but learns that Shaun is in the Institute's hands. While searching for a way to gain access to the Institute, the Sole Survivor begins interacting with the other factions, including possibly joining the Brotherhood of Steel, becoming an agent of the Railroad, rebuilding the Commonwealth Minutemen with Preston Garvey as its General, or possibly some combination of the three. After succeeding in breaking in, the Sole Survivor learns that their son is actually the leader of the Institute, Father, who wishes for them to join him.

With the Sole Survivor getting unlimited access to the Institute, they become an important asset to the Brotherhood of Steel, who wish for information from their computer network, and the Railroad, who request the Sole Survivor make contact with an inside agent, Patriot. If the Sole Survivor chooses to help these factions, conflicts between them will begin to escalate, such as the Institute attacking the Railroad's interests in Bunker Hill, resulting in a potential three-way battle between the Institute, Railroad, and Brotherhood of Steel. The Institute also may assault and wipe out one of the Railroad's safehouses, Ticonderoga.

With the Institute requiring additional power, they attempt to take over the Mass Fusion building, resulting in a battle as the Brotherhood of Steel attempt to stop them. The Brotherhood of Steel also begin plans to rebuild Liberty Prime, their most powerful weapon. The Railroad meanwhile hope to work with the Sole Survivor to prepare a mass breakout of synths from the Institute.

Eventually, the Sole Survivor will be forced to pick a faction to truly side with. The Institute will name the Sole Survivor their new leader, and have them wipe out the Railroad's headquarters and reprogram Liberty Prime to destroy the Prydwen. The Railroad, alternatively, will sneak onboard the Prydwen and destroy it from within, then launch their synth breakout before destroying the building. The Brotherhood of Steel will also have the Sole Survivor to wipe out the Railroad headquarters then use Liberty Prime to forcibly break into the Institute's facility.

Finally, if the Sole Survivor angers the Institute, they can have the Minutemen wage war against them. While this will result in the Institute attacking the Castle, their members will be able to sneak into the Institute and destroy it from within.

Aftermath
Following the end of the main conflict and the destruction of one or more of the fighting factions, the faction the Sole Survivor chose to side with will become the dominant force in the Commonwealth. They will also take over Diamond City, with their flags flying over the city and their troops patrolling the streets. A conflict can also start between the Commonwealth Minutemen and Brotherhood of Steel, with the Brotherhood attacking the Castle and settlements after the Minutemen take down the Prydwen with their artillery.