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.

Background
After years of development, the Institute succeeded in the creation of generation 3 synths, automatons almost completely identical to humans, in the late 2220s. In the years following, the Institute began sending these synths out to infiltrate the Commonwealth, by either simply giving them false identities or "replacing" wastelanders with synth copies of themselves. The existence of these synths became known to the people of the Commonwealth in an event known as the Broken Mask incident in 2229, where a synth malfunctioned, shot, and killed several people in the Diamond City marketplace. This served as the official introduction between the synths and the people of the Commonwealth, and ignited fear and paranoia across the wasteland over the possibility of being replaced or having a loved one replaced. This fear and paranoia was worsened by the CPG Massacre sometime in the 2230s, in which various settlements across the Commonwealth were attempting to band together and form the "Commonwealth Provisional Government," with the Institute trying to help with the planning. During a meeting in which a synth attended, all parties were killed by some party (possibly the Institute), and the Institute was subsequently blamed. Other events occurred that increased tensions further, such as the destruction of the settlement of University Point by the Institute in 2285.

Due to the Institute's belief that synths are no more than tools, and that those that show emotion and try to escape the Institute are no more than malfunctioning tools, an organization known as the Railroad was founded sometime after the Broken Mask incident in order to liberate them. Believing synths to be sentient, the Railroad began rescuing synths from the Institute and hiding them away across the Commonwealth and beyond, by either wiping their mind and giving them new identities, or by creating distance between the escaped synths and the Institute. They also established a relationship with a mysterious figure within the Institute that they designated as "Patriot," who began releasing and sending them synths for rescue. The Institute, seeing the Railroad as a misguided annoyance, launched attacks whenever possible, such as the Railroad Safehouse Raids. in early 2287. As a result of these raids, the Institute succeeded in crippling a large number of the Railroad's operations across the Commonwealth by depriving them of members and resources, as well as a number of their safehouses and their then-headquarters. This forced the remaining leadership to evacuate and form a new headquarters in the catacombs of Old North Church.

In that same year, a Brotherhood of Steel recon squad, the third Brotherhood excursion into the Commonwealth, detected high energy readings coming from the Institute and broadcasted its findings to the Capital Wasteland. This caused Elder Maxson to deploy a full expeditionary force with the Prydwen to the Commonwealth to personally investigate what the Brotherhood believed to be a threat to humanity. Considering synths to be abominations and a clear attempt to tamper with humanity, the Brotherhood began investigating the Institute in preparation to destroy them.

Even though the Railroad had been in conflict with the Institute for sometime, the arrival of the Brotherhood posed a serious problem for them in the long run; they feared the Brotherhood may target safehouses where the Railroad was trying to get defecting synths out of the Commonwealth in order to achieve their goal of wiping out all synths. Conversely, the Brotherhood has dealt with the Railroad in the Capital Wasteland, and knows they may pose a threat to their operations in the Commonwealth, as they clearly ideologically 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 than solutions. Thus, at the very least running each other out of the Commonwealth will bring their vision of "peace" quicker.

Also in 2287, the Quincy Massacre occurred, in which the settlement of Quincy was attacked and destroyed by the mercenary band known as the Gunners. The once powerful but long-ailing citizen's militia known as the Minutemen attempted to defend the town, but due to infighting, betrayal, and small numbers, were mostly wiped out. A small contingent of Minutemen led by Preston Garvey, a then mid-ranking member of the Minutemen, evacuated the town with a number of civilians and fled in the direction of Sanctuary, while being pursued and having many killed by Raiders and feral ghouls on the way. By the time the group reaches Concord, they are surrounded by Raiders and the organization is down to only one member and a small group of civilians, effectively ceasing to exist.

While the tensions build, the Minutemen can rebuild and potentially become a major player in the war led by the Sole Survivor. With no faction openly hostile to them, the Brotherhood, Institute, and the Railroad will begrudgingly allow them to grow in power and strength, and lead a peaceful, but tense, coexistence.

War
When the Prydwen arrived in the Commonwealth, the Brotherhood established a permanent base at Boston Airport after wiping out the ghouls there, and then linked up with the recon squad to establish another outpost at the Cambridge Police Station. They may also launch an attack on the nearby super mutant controlled Fort Strong in order to secure the munitions there. The arrival of the Prydwen led to increased hostilities throughout the Commonwealth, including the Brotherhood investigation of the C.I.T. ruins and subsequent hostile 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, who had been frozen in a cryopod for over two hundred and ten years, became involved in the conflict. Some time during their Vault's cryogenic stasis, Conrad Kellogg, an Institute enforcer, and two other Institute members broke into Vault 111, killed the Sole Survivor's spouse and kidnapped their son, Shaun. After awakening from cryostasis and searching for Shaun, they eventually confront and, after learning that Shaun is being held by the Institute, kill Kellogg. 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, or possibly some combination of the three.

If the Sole Survivor elects to rebuild the Minutemen, they will help Preston Garvey recruit settlements across the Commonwealth and retake the former Minutemen headquarters known as The Castle, swelling the resources and manpower of the organization rivaling its old glory days. They may also rediscover the Minutemen artillery schematics, allowing the Minutemen to strike anywhere in the Commonwealth with artillery with ease. This includes the Prydwen, making the Brotherhood uneasy.

Whatever the Survivor decides, they eventually find a way into the Institute, and it is revealed their son Shaun is in fact the administrator and director of the Institute, who is known as Father. From this point on, the Sole Survivor decides who to take sides with, which then decides the victor in the conflict.

The Sole Survivor is given unlimited access into the Institute, becoming 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 the town of 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.

Both the Brotherhood and the Institute require a large amount of energy to either power Liberty Prime or provide a permanent power source for their underground laboratory respectively. Whoever the Sole Survivor decides to help, they head to the Mass Fusion Building and helps either Proctor Ingram or Allie Filmore secure the huge nuclear reactor, battling opposing forces along the way. After securing the reactor, they are prepared to finally take the fight to the enemy.

If they sided with the Brotherhood, they will wipe out the Railroad and use the newly repaired Liberty Prime to blast a hole in the ruins of the C.I.T. ruins and destroy the Institute from within using their decaying nuclear reactor.

If they sided with the Institute they will wipe out the Railroad and then launch an attack on Boston Airport, where they will hack Liberty Prime to recognize the Prydwen as a "Communist" vessel and destroy it.

If they sided with the Railroad, the Brotherhood will launch a failed attack on Railroad HQ, causing the Railroad to counterattack by destroying the Cambridge Police Station, stealing a Vertibird, infiltrating the Prydwen using it, then setting three blast charges in the main deck of the ship, destroying the warship. After removing the Brotherhood as a threat, they will infiltrate and assault the Institute using an inside contact, stoke a synth uprising, and then destroy the facility using their nuclear reactor, all the while rescuing the synths there.

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 using their nuclear reactor.

Aftermath
The faction who wins the conflict will become the dominant force in the Commonwealth. Forces of the victorious faction can be found patrolling and manning military checkpoints all throughout the wasteland. The Sole Survivor can assist in the defense of these checkpoints. Diamond City will also be controlled by the given faction, with their respective flags being displayed over the city and a number of their forces establishing a presence in the marketplace. For example, siding with the Brotherhood will occupy Diamond City by placing a Knight browsing the stores and a Senior Scribe in front of the noodle shop. Conversely, siding with the Institute will place two generation 1 synths in the city, idly using work benches and browsing shops.

If the Institute is destroyed by either the Brotherhood or Minutemen, and the Brotherhood subsequently becomes hostile to the Sole Survivor, a conflict can begin between the Minutemen and Brotherhood, with the Brotherhood attacking the Castle and other settlements after the Minutemen take down the Prydwen with their artillery.

Optional battles

 * Battle of Bunker Hill
 * Battle of the Institute
 * Second Battle of the Castle
 * Battle of Boston Airport
 * Shelling of the Prydwen