So, I'm pretty sure that people who did Railroad and Institute playthroughs were shocked to see the Prydwen in 2296. More importantly, it seems as if the numbers of the Enclave and the West Coast Brotherhood have been bolstered. I believe that by 2296, the Brotherhood controls the Boston Commonwealth and allied themselves with the Minutemen to recruit settlers. As for the Enclave, it's safe to assume the remnants of the Institute fled with their archived information in tow and formed an alliance with the Enclave remnants. What remains of the Railroad could have joined up with the NCR, though I'm not sure if they'd see eye to eye. Of course, I could be wrong as well.
What direction do you all think season two will take?