During the cop ending of Gat out of Hell we see Kinzie and Matt interrogating a character named "Brimstone" who's face is completely obscured, now this is important because the leader of the Mayhem organization in AOM is referred to as Brimstone and appears to be the French Female Boss from SR4. Another important thing to take note is that both Mayhem and Legion appear to be using a mix of STAG, Zin, and Syndicate technology. So here's my theory for the new timeline. SR1 happens as normal but at the end of SR2 the Boss decides to blackmail Vogel with the info about the nanite experiments, Masako and The Pyramid instead of straight-up killing him. This in turn causes a much more uneasy relationship between the Saints and Ultor than what we see in SR3. Fast forward to SR3, the Saints and Ultor still merge, but in order to avoid controversy Ultor merges the remnants of the Masako Units with the Saints and rebrand them as Mayhem. STAG and the Syndicate still exist but this time the Syndiacte are even more powerful than they were in SR3, Matt joins the Saints\Mayhem alongside Kinzie, Gat isn't captured\killed and is now the second-in-command of Mayhem, Kilbane and his Luchadors launch a series terrorist attacks throughout Stilwater, and STAG is given even more funding to combat the other groups. However at the end of SR3 STAG is still disbanded and the Syndicate have been crippled. During the events of what was supposed to be SR4 the Zin have went from a mighty empire to an extinct species, however somehow an Old Zin aircraft containing a massive amount of alien tech and information crash lands on earth. Coincidentally a bunch of ex-Syndicate and STAG grunts discover this tech, form the terrorist group known as Legion and decide to launch a violent coup, taking over most of the world through assassinations, terrorist attacks, back-ally deals and rigged elections. Thus begins AOM. Finally at the end of AOM something happens with Mayhem that causes Brimstone to be arrested by an unknown group which finally leads into the cop ending for GOOH.