War for the Commonwealth

The War for the Commonwealth was a major armed conflict in the former Commonwealth of Massachusetts, where the forces of the East Coast chapter of the Brotherhood of Steel clashed with the Institute, while the Commonwealth Minutemen attempted to restore and unify the region, with the secretive Railroad pursued its own agenda.

Background
The War is tied directly to the single most powerful polity in the Commonwealth, the Institute. The Institute formed out of the ashes of what was once known as the Commonwealth Institute of Technology (CIT). While the college itself was completely destroyed in the flames of the Great War in 2077, the science staff took refuge in the underground of the Institute and carved out a subterranean habitat for themselves. The Institute was formally founded in 2110, as the children of the original survivors dug into the earth and built increasingly sophisticated habitats and laboratories, starting an ongoing process of expanding the Institute's facilities and infrastructure.

Isolated from the outside world, the scientists continued their work, disregarding the mayhem and destruction occurring outside of its grounds. As they worked on creating synths, they attempted to work peacefully with the people of the Commonwealth using first generation synths, but mutual mistrust ended that relationship quickly and they returned to isolation. The creation of the molecular relay (teleporter) in the 2180s allowed the Institute to seal itself off from the surface permanently, while major strides made in robotics allowed them to usher in the second generation synths. For decades, the first and second generation synths were the most visible part of the Institute's operations, scavenging for materials and performing experiments on the surface, while the scientists lived their lives in comfort and safety, sheltered within the utopian Institute.

To overcome the mechanical limitations of second generation synths, the Institute dedicated nearly 50 years to creating an organic replacement, using FEV and captured wastelanders as basis. Due to radiation-induced changes in the genetic code of all post-War humans, they hit a brick wall until the acquisition of Shaun in 2277. A pre-War infant kept in stasis at Vault 111, Shaun's DNA became the basis of the third generation synths. The infant Shaun became Father to a whole family of engineered super-beings. Of course, tests were not without setbacks - in 2229, a defective 3rd generation infiltrator caused the Broken Mask Incident, permanently vilifying the Institute in the eyes of the Commonwealth, and causing no small amount of internal problems for the Institute, as he was sent out without proper testing or approval.

Since then, the Institute continued developing technologies and pushing back the boundaries of science, using their technological superiority and industrial capacity to operate uncontested. The only potential opposition, the Commonwealth Minutemen, have declined due to internal disputes and politicking, with the fall of The Castle in the 2240s only hastening their demise. As such, the Institute was free to exploit the Commonwealth as a source of raw materials, salvage, and technology. What could not be salvaged or stripped apart, would be used in experiments ranging from agriculture to bioweapons. Any settlement that refused to hand over anything the Institute was interested in faced destruction, with those that did cooperate still at risk of extermination should they be used in any Institute experiment. Everyone else is also at risk of being targeted, as the Institute abducts humans and replaces them with infiltrators to keep an eye on the surface or sow discord and disorder - as was the case when they captured a Diamond City resident and engineered a campaign to install him as mayor of the City. His first decree resulted in a pogrom of ghoul citizens.

Railroad opposition
An organization of unknown provenance, the Railroad was the only Commonwealth organization directly fighting the Institute, at least since the introduction of third generation synths shortly after 2227. Repeatedly destroyed by the Institute, the Railroad always managed to come back, reorganized and stronger after it escaped oblivion yet again. The latest incarnation was reformed in 2266, after failures in maintaining operational security revealed the location of their headquarters to the Institute. Over the next twenty years, the Railroad rebuilt, implementing lessons paid for with blood, surviving two more leaders until Desdemona came to the fore around 2277. She introduced major changes to maintain operational security and acquired two of the most important assets in its history: Tinker Tom and P.A.M. Tom's technical genius coupled with P.A.M.'s predictive logic and analysis capabilities allowed it to expand its operations and intensify operations - and even survive another crackdown in 2281. Although the loss of Switchboard was a heavy blow, the Railroad did not fall apart. The emergence of an Institute insider in 2283, code-named Patriot, and the subsequent decoding of his messages supercharged the Railroad, allowing it to rescue synths on a large scale - over thirty between 2283 and 2286.

Brotherhood of Steel involvement
Between 2280 and 2287, the Brotherhood sent three recon missions into the Commonwealth. The first scout team was overwhelmingly successful: They brought back crates full of pre-War technology and documents and the first post-war reconnaissance of the area.

The second mission in 2284 was carried out by Recon squad Artemis under Paladin Brandis. It was Artemis was not so fortunate with their problems beginning at their drop-off point in Malden. Ambushed straight off the Vertibird, the team was forced to scuttle their armor, losing four Knights. The survivors made their way to the National Guard training yard to regroup, but were forced to retreat due to feral ghouls, losing another Knight. Paladin Brandis and his Scribe left to investigate the pre-War Revere satellite array, but super mutants present on site overwhelmed them and claimed the Scribe. Brandis was the only survivor, retreating to recon bunker Theta and trying to survive until relief arrived.

Three years later, Recon Squad Gladius, under the command of Paladin Danse, deployed to the Commonwealth under the same orders as Artemis, with the added objective of investigating the previous squad's disappearance, if possible. As with Artemis, they encountered a substantial amount of resistance from raiders, resulting in the loss of four knights. Over the course of several weeks, they managed to secure a base of operations at the Cambridge police station. Upon discovering advanced signals originating from the Institute, Danse sent an emergency signal to the Brotherhood requesting reinforcements. The Brotherhood responded by rapidly mobilizing the chapter and sending the Prydwen to the Commonwealth. The airship arrived just as the Sole Survivor dealt with Conrad Kellogg, passing over Fort Hagen and Boston under Vertibird escort, sending a message to the Commonwealth and the Institute. The Brotherhood established a permanent foothold at the Boston Airport and bolstered Gladius' position at the police station. The campaign to destroy the Institute and the threat it posed to humanity began.