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. They also recieved reports of an unknown Super Mutant variant and their activities around the Commonwealth, and finally the first recon squad (led by Paladin Brandis) sent to the Commonwealth failed to report back on time. This series of events left Elder Maxson no choice but to personally investigate, by literally flying the Prydwen over the entire Wasteland, setting up camp at the ruins of the Boston Airport, and began to consolidate his forces; first and foremost, for the purpose of investigating and eventually destroying the Institute, as they have tracked both the source of Super Mutants in the region and, more importantly the manufacturers of synths; they consider synths a clear attempt to tamper with humanity, (which in the Brotherhood's history with West-Tek and FEV, they consider a serious danger to peace and stability in any region), as well as, as Maxson puts it, "humanity's curiousity getting ahead of its restraints," which in the Brotherhood's eyes, led to the Great War in the first place.

Even though the Railroad has been in conflict with the Institute for sometime, the arrival of the Brotherhood poses a serious problem for them in the long run; they fear the Brotherhood may target safehouses where the Railroad is trying to get defecting synths out of the Commonwealth in order to achieve their goal of wiping out every synth in existence. Conversely, the Brotherhood has dealt with the Railroad in Capital Wasteland, and knows they may pose a threat to their operations in the Commonwealth, as they clearly idealogically oppose the Brotherhood's goals. Thus, while their primary enemy is the Institute, they both feel peace either is not a strategical option or will bring more problems then solutions. Thus, at the very least running each other out of the Commonwealth will bring their vision of "peace" quicker.

Meanwhile, the Minutemen, named after the first fighters who fought for freedom in what is now the Commonwealth, once nearly annihilated by the infamous Quincy Massacre, have started rebuilding their numbers, and have started becoming stronger as the three factions pick away at each others ranks in clashes and skirmishes around the Commonwealth, something that has not gone unnoticed by any of them.

War
The arrival of the Brotherhood's warship raised tensions around the wasteland; both the Railroad and the Institute were clearly intimidated by this obvious threat to their dominance and survival in the Commonwealth, and bypassers who saw the huge airbase soar through the skies announcing their goals of peace for the wasteland as a whole were just confused. The Minutemen, shaken for a moment, continued to make gains in the Commonwealth.

At one point, the pre-War individual known as the Sole Survivor, who had been frozen in a cryopod for over two hundred ten years, became involved in the conflict. Some time during their Vault's cryogenic stasis, a group of what seemed to be mercenaries entered the Vault (unopposed, since the Vault's staff and security had engaged in a Vault-wide civil war and killed each other off), broke into their partner's stasis pod, killed their partner, and stole their son. Searching for their lost son, Shaun first going to Concord, where the last Minutemen are pinned down by raiders, then to Diamond City, where they save and then hire a private detective named Nick Valentine whose leads eventually take him to Fort Hagen, a seemingly abandoned military fort. Upon investigation, it is revealed that the derelict fort is not only an Institute observation outpost, but also the hideout of Kellogg, the man who had kidnapped the Sole Survivor's son. After fighting their way through the fort, they finally confront and, after extracting information from him, kill Kellogg. Their revenge for their husband complete, they required the resources to access the Institute; yet no one actually knew how, outside the Institute themselves. This is when the Brotherhood flies the Prydwen in from the Capital Wasteland and the war evolves from a cold war between two factions to open war between three.

The arrival of the Brotherhood is not entirely negative; they potentially possess the resources to build a device that can teleport them into the Institute. Conversely, so do the Minutemen and the Railroad. Whatever the Survivor decides, they do eventually get into the Institute, and it is revealed their son is, in fact the administrator and director of the Institute, referred to by synths in the Institute as "Father," as his genes were required to create Generation 3 synths, which also reveals the reasoning behind his kidnapping.

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.