Most info from Wikipedia:The Ultimates:
Hank Pym is under house arrest at Ultimates Mansion. One of Pym's Ultron robots drugs him and leaks a sex tape of Stark and the Black Widow to the Internet. These distract from the robot's fatal shooting of the Scarlet Witch. Magneto abducts Wanda's corpse and retreats to the Savage Land, where he is confronted by the Ultimates. Pym and Wasp discover the truth about the Ultron robot, which has adopted the identity of Yellowjacket and uses the Ultimates' DNA to create a series of android duplicates. Although the true Ultimates destroy their android counterparts and Yellowjacket, Quicksilver is apparently killed by Hawkeye. The Wasp then invites Pym to return to the Ultimates, and he accepts. The mastermind behind the robot's plot is revealed to be Doctor Doom.The Ultimate Fantastic Four:
In "Think Tank" the team meet Rhona Burchill (a re-imagined Mad Thinker), who captures them and attempts to sell them to the highest bidder. In "Ultimate Fantastic Four Annual 1" they meet Crystal of the Inhumans, and as a result of trespassing on their home destroy it, forcing the Inhumans to move to a new one. "Crossover" has them encountering zombie infected versions of themselves and every other hero of that world. With the help of that world's Magneto the Fantastic Four manage to escape with the few survivors. "Tomb of Namor" has the Four encountering Atlantian criminal Namor who only leaves when he gets a kiss from Susan Storm. In "Super-Skrull" Reed Richards goes back in time to the teleportation accident to ensure it doesn't go wrong. There is dispute amongst the team to whether this is the right course of action. However, after a cruel prank played by Johnny Storm on Ben Grimm, the team realize just how depressed Ben is being trapped inside 'The Thing'. Reed goes back and makes the experiment a success. We then see how the time-line has been altered. Everyone on the planet except Ben has superpowers thanks to the Skrull pill given to them by the Skrulls and the leader Super-Skrull. The Skrulls however have tricked humanity and the still-human Ben Grimm is their last hope. In "Frightful", Johnny is infected with an illness only Doctor Doom can cure; it also features the escape of the Frightful Four. In "God War," alien terrorists attack Reed, who is looking for a seed while also facing a powerful enemy. The next arc "Devils" introduces Diablo who kidnaps those close to the four as bait; he intends to get immortality by using Reed's sister as a power source. It appears that after the events in Ultimatum that this book along with Ultimate X-Men will be cancelled.The Ultimate X-Men:
Vaughn's tenure as writer on Ultimate X-Men was followed by Robert Kirkman, author of The Walking Dead and Invincible. Kirkman's tenure was noted for adapting several major story arcs from the regular X-Men series. These included Jean Grey's transformation into Phoenix, the arrival of Cable and Bishop, and the appearance of Apocalypse. Kirkman reintroduced Wolverine as an important character and played with issues of team loyalty. Under his authorship major characters such as Nightcrawler and Colossus left the team. His tenure also featured Cyclops' decision to turn Xavier's into a more traditional school and consequently disband the X-Men. When this was done an alternate team of X-Men was formed by Bishop as part of the upcoming fight against Apocalypse.
It has recently been announced on marvel.com that in February of 2009 the series will reach its conclusion. The future of the Ultimate X-Men is unknown at this time as several other Ultimate Marvel imprints will still be published.Ultimate Spider-Man:
Eventually, several 'mainstream' characters were introduced into the story. Bendis, disliking the mainstream version of Venom and its extraterrestrial origin, completely reinvented the character.
On August 16, 2006, Mark Bagley announced he would be leaving the book as of Ultimate Spider-Man #110. Bagley and writer Brian Michael Bendis worked on the series together since it began. Artist Stuart Immonen, already famous in the Ultimate Universe for his work on Ultimate X-Men, took over after Bagley. Issue #111, named "The Talk", introduced readers to Immonen's art for the first time. The issue was divided into two parts, with Bagley covering the art for one section, and Immonen doing the other. Issue #133 of the series is the final issue of the series but it will be rebooted as Ultimate Comics Spider-Man.Ultimate Magneto:
Most recently, Magneto has shown up in the "Aftermath", following the death of Charles Xavier. Magneto has apparently freed Forge from prison, and there are signs that he is building something. Exactly where he is hiding is still unknown, but with Charles Xavier's death he now believes it's time to speed up his plan. He takes pleasure knowing his former friend is dead (unaware that he is in fact alive and was simply transported into the future). He has a close relationship with Mystique, and arranged for her to be freed from the Triskelion by having Mastermind take her place. He has also apparently established a mutant commune. He appears in Ultimates 3 along with the Brotherhood (Mystique, Blob, Sabretooth, Lorelei and Madrox). They attack the Ultimates Mansion so he can talk to Quicksilver about re-joining the Brotherhood and retrieve Wanda's body. Magneto appeared in Ultimate Spider-Man and revealed that the Blob is Liz Allan's father. He tried to recruit her into the Brotherhood.
In the cross-over event Ultimatum, Magneto has caused global devastation, killing millions of people, both mutant and human. He is shown wringing Professor Xavior's neck, killing him in the actThe Ultimate Brotherhood:
In the Ultimate War and "Return of the King" storylines, Quicksilver and Scarlet Witch defected to the Ultimates (mirroring their earlier defection to the Avengers in the mainstream Marvel universe) to help stop the resurfaced Magneto. The ranks of the Brotherhood were now strengthened by Destiny, Unus, Juggernaut, Hard-Drive, Rogue, Sabretooth, Vanisher, Forge and Multiple Man. After being defeated by the X-Men yet again, the Brotherhood receded for a time. Recently, they seem to have restarted their activities, beginning with the newly-introduced Mystique and Forge's plan to free Magneto from his plastic prison cell in The Triskelion with Mystique taking his place to prevent anyone from realizing that Magneto is free. After the events of the "Magnetic North" storyline, Longshot seems to have joined them. At the beginning of the "Sentinels" storyline, Mystique is replaced by Mastermind and his new girlfriend, Stacy X.
In The Ultimates 3, the members have changed slightly, with Sabertooth leading Blob, Unus, Madrox, Mystique, Venom and new member Lorelei. Magneto again is the leader of the team, but doesn't join the fight.Ultimate Dr. Doom:
Reed, having studied Doom's magical texts, returns to New York to battle the concurrent threat of the alternate universe zombie Fantastic Four. Reed is willing to lose himself in the dimensions to erase the zombie threat but Doom switches their bodies back and does so. His last request is to be remembered as the one who saved the world. However this was not granted.
He has since reappeared in issue six of Ultimate Power, a crossover between the "Ultimate Universe" and the universe of the revamped Squadron Supreme, seemingly intent on taking over the Supremeverse. In issue eight it is revealed to be simply a Doombot (the first seen in the Ultimate Marvel continuity). The real Dr. Doom is later seen in Ultimates 3 as the one controlling Ultron. Yet it was never explained how he escaped the zombie universe alive. It is noted however, that, starting in Frightful and through his "Ultimate Power" and "Ultimates 3" appearances, his 'goat legs'are not present, but resembles his regular 616 counterpart a bit but not by much. As to why his former look has been abandoned is yet to be revealed