[b]Plans for the Commonwealth Arc[/b]

Basically, the starting difference between this Commonwealth and the one in Canon is the fact that the Sole Survivor got killed along with his wife, leaving Shaun/Father a complete orphan (another, OOC reason is that the Sole Survivor is the most railroady of the Fallout Games' protagonists, aka his plot is the most forced). 

The second difference is that Marie Ashur (daugther of Ashur from Fallout 3, and who got aged up from 10 to 20 in this universe), an unmutated human, succeeded her father as the leader of the Pitt, and needing allies against the Brotherhood and further Slave Uprisings, as well as hearing that Shaun is also an unmutated human, allied with the Institute, providing both brawn and a brain that wasn't cooped up in an ivory tower and thus not walled off from the realities of the world.

With Marie Ashur's support, perhaps even coddling, The Institute began pursuing a more militant policy against The Railroad and Minutemen, exterminating the former and reducing the latter to just Preston, who was forced to seek refuge in the Brotherhood, which itself was being pressed from two fronts; the Pitt itself was paying raiders to attack the Capital Wasteland as the more militant Institute was attacking its Commonwealth holdings. This pushed the Brotherhood in the Capital Wasteland to adopt a more 'liberal' and 'inclusive' policy towards Ghouls and Super Mutants, because it needed the manpower to stretch itself across DC, New York, and The Commonwealth.

Seeing this, and finding the Institute - Marie Ashur Alliance to be a threat, the Book Runners (they sell guns too), led by Peter and Miranda Rapids, began gathering together a council of local power groups in Boldt Castle* in order to aid the Brotherhood/extort concessions from it. Sarah Lyons will also attend said conference, as well as the PCs, where they will be attacked by a fleet of raiders, hired by the Institute to disrupt the proceedings ([b]Edit:[/b] This might be Retconned out to provide more time for Character Development).

Anyway, the Pyrdwren will go on to the Commonwealth with the PCs in tow, and said PCs will begin turning the tide, either by creating a New Railroad that would help the ordinary people of the Wasteland as well as Synths, or helping Preston rebuild the Minutemen, or attacking the Institute directly.

But, there is one final battle. Marie Ashur, realizing that the Brotherhood is regaining ground, is going to go to the Commonwealth herself with an army to help Shaun. And, with her defeat, the RP ends.

*https://en.wikipedia.org/wiki/Boldt_Castle