The main plotline of the storyline will concern Magneto and Dr. Doom, who has returned from the Marvel Zombies reality without any explination. Magneto will confront Dr. Doom for being responsible for Wanda's death, but Ultimate Impossible Woman (not Man, Woman) will be introduced and the three will have a threesome because Loeb loves writing smut into comics. They will all then decide that their goal is to screw around with the heroes and mutants, because they are the mutual enemies of Magneto and Doom, and Impossible Woman thirsts for chaos.
In Ultimate Spider-Man, Uncle Ben and Captain Stacy will return. They will both promptly turn out to be Doombots, as well as Captain Stacy being Ultimate Anti-Venom. The Green Goblin, who is alive after all, and is in on the menacing with Doom and Magneto and is specifically trying to torment Peter. The Jackal, Morlun, Mister Negative, Hydro-Man, and Klaw will all be introduced as minor enemies which Spider-Man takes out in a few pages at the start of each issue. None of them will have to do with anything, and will be there just because. The reason Ultimate Spider-Man Annual #3 has the "March on Ultimatum" banner on it is because Mary Jane will reveal to Peter that she is pregnant, with the baby being conceived during the Annual.
In X-Men, half of the X-Men will turn out to be addicted to Mutant Growth Hormones, which in the UU literally makes mutants grow. So Rogue, Nightcrawler, Dazzler, Iceman, Beast, and Firestar will spend the entire time running around at Giant Man size and attacking skyscrapers without reason. The MGH will have been created by Magneto from the Wasp's DNA, and the DNA-stealing process is what changed her from Asian to white. Wolverine will spend the length of Ultimatum trying to stop his teammates, while at the same time discovering the reason he and Sabretooth are rivals is because of their hair colors and he will shout "WHAT THE #@$&?!" every five pages. Xavier, meanwhile, will be hanging out at small town bars trying to pick up underage girls.
UFF will still remain incredibly boring and nobody who reads it will remember what they just read three minutes after putting it down.
It will all come to a head in the main series where all the heroes board a Helicarrier and go into outer space to find Ultimate Beyonder, who is a Doombot that went out of control and has Phoenix-level power. All the characters will run around aimlessly and Spider-Man will fail horribly at cracking any jokes while meanwhile Thor decides that it would make the most sense if he were to speak in Anglo-Saxon. Ultimately, Rick Jones will appear near the climax, blast Beyonder will a death ray, and everyone will return to the Trisk and celebrate. Then Mephisto comes and gets Spider-Man to agree to retconning reality so that none of this ever happened and Mary Jane isn't pregnant (because promoting divorce or abortion is bad, so we need to magic it away). The end.
I'm going to regret this post tomorrow morning, I know it.