"Established, popular characters? Check. Reinterpretation of a beloved, classic storyline? Check. Stretched-out presentation of the same? Check. Helmed by a popular creator of original works in his own right? Check. Updated characterizations that sometimes toy with the original creator's personas? Check. A bigger, more contemplative/brooding/generally 'big' tone? Check. Yeah, it's an Ultimate book, at least as we know them now."
A kind of "reboot" designed to create an Adaptation Distillation effect in the same medium as the original. Said adaptation will usually incorporate bits of plot and design from each previous incarnation, but is overall a standalone world/story that can be understood by newcomers. A more specific and very deliberate form of Alternate Continuity.
Extremely common in RetooledCross Overs, as this allows a more precise meshing of plots than a Retcon may allow.
They may usually contain several Mythology Gags, referencing things from the original work (either as a remake of popular plots or circumstances, or as a mere detail that the fans may notice and the new readers may not even notice as such). If both universes are being used, the original and the ultimate, the ultimate universe may take more liberties than the original: for example, an important character may be Killed Off for Real, because Status Quo Is God only at the original universe.
Named for the Marvel Comics "Ultimate Marvel" line, which sought to update and streamline decades of continuity with a reboot but without canceling out the original storyline. Most superheroes under the "Ultimate" umbrella brand are given reboots of their own, but on a smaller scale — Spider-Man's 'radioactive spider' origin story was replaced with an updated 'genetically engineered spider' version.
The "Ultimate" line, it should be noted, was intended to present Marvel's flagship characters to a new, modern audience; the rationale behind the quasi-reboot was that new readers to those series would be lost when confronted with nearly 30 years of backstory (though after ten years and running, Ultimate Marvel is developing quite a backstory of its own).
Fan Fiction writers frequently do this in Alternate Universe Fics, essentially rebooting the mythos to incorporate their own ideas, Fanon, and other material.
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Anime and Manga
ROD the TV: Mainly retooled the Read Or Dream manga's basic story to fit into the storyline done in the Read or Die OAV.
Bubblegum Crisis: Tokyo 2040 is a deep reboot of the classic anime OAV series Bubblegum Crisis. However, so many changes were made, from character designs to backstory to the overall plot, complete with a pseudo-Gainax Ending, that most fans of the original series were rather unimpressed with the end product.
SEED is a more explicit example, as it bears a lot of similarities to the original series and is sometimes called "21st Century First Gundam" by Sunrise* First Gundam is a semi-official nickname for the original show.
You can generally tell which series are examples by how big the focus is on their respective GUNPLA line. Seed and 00 have entire separate lines dedicated to them, making them stand out even more as reboot series.
There was also For The Barrel, an obscure Light Novel-styled story featured in Newtype magazine with radically redesigned characters and mecha.
Naoki Urasawa, creator of Monster, did this for Astro Boy with Pluto. One reviewer explicitly compares it to Ultimate Marvel (see page quote). The 2003 animated series also arguably qualifies, as it took many of the unrelated storylines from the largely continuity-free classic manga and wove them together into a cohesive story-arc.
The Tenchi Muyo! OVAs have two: Tenchi Universe, which has all the main characters and more or less a basic outlining of their backgrounds, plus an another character and the same Big Bad and Tenchi in Tokyo, with pretty much the main characters in the latter.
Go Nagai's Devilman series possibly qualifies - there's a comic series, 1970s anime TV series, and three linked OVAs released between 1987 and 2000; each one of them retells the same events but in an updated, refined, condensed way. And, of course, there's Devilman Lady, which is something of a combined ultimate edition and full-on reboot...
The Naruto Movie, Road to Ninja, appears to be based off this, featuring an earth with Naruto's parents living and alternate personalities for each character, though their histories and romances appear to be similar to the mainstream Naruto's.
The DC Comics "All-Star" line, which had the All-Star Superman and All-Star Batman & Robin The Boy Wonder miniseries (with future projects based on Wonder Woman, Batgirl, and possibly the Flash), is a form of this. The series aren't supposed to take place in any particular continuity (although All-Star Batman and Robin does supposedly take place in the same continuity as Frank Miller's other Batman stories), and are supposed to be a concentration of what makes those characters special. As well, Justice is basically All-Star Super Friends, even if it couldn't legally be called that.
The two upcoming series of trade-paperbacks Batman: Earth One and Superman: Earth One are following the Ultimate Marvel formula more closely than the All-Star line, intending to be a modern reboot in a new continuity rather than mini-series written outside of continuity.
As of March 2014, there will be a Wonder Woman: Earth One and Teen Titans: Earth One coming.
The New 52 relaunch also has some of this, but confusingly not always. Some series are just continuations of old series with renumbered issues while others are complete reboots or retellings. Can be quite confusing to tell which is which at times. Ironic, as the whole point of the New 52 was to make things less confusing for new readers.
Devil's Due productions attempted this with G.I. Joe Reloaded.
Mega Man Reawakened takes elements from every version of Mega Man to create an original universe.
Mega Man Recut is one for the cartoon and the games, with every Robot Master set to appear and a heavily layered plot.
Man of Steel is seen as this for the Christopher Reeve Superman films and Superman movies as a whole as it takes place in an entirely different universe and providing a more modern take to the Superman story.
The Amazing Spider-Man could be said to be an Ultimate Universe to the Sam Raimi Spider-Man Trilogy. Appropriately, while they both draw from both continuities, Amazing seems to be leaning more towards the comics Ultimate Spider-Man.
The 2009 Star Trek movie ("Star Trek XI") and its sequel. They take place explicitly in an Alternate Timeline compared to the TV shows and the earlier films, created via time travel in the first film, but show all the hallmarks of an Ultimate Universe in terms of retelling iconic storylines in a more "contemporary" style.
The sequels to 2001: A Space Odyssey are all set in the universe established in the film version (the mission terminates at Saturn in the novel, at Jupiter in the film), but each one is set in a somewhat divergent universe that does not necessarily take all events of the previous novel(s) into account. Thus 2061 diverges from and ignores the epilogue of 2010, and 3001 glosses over several major implications described in the three previous novels. Clarke stated in the introductions to all three sequels that this was deliberate.
In Once Upon a Time, the Land Without Magic (aka Storybrooke) could be considered this. Individuals who in their realms were contemporaries of each other, have existed as stories in our universe for hundreds, if not thousands of years.
Several campaigns by RPGA managed to receive the Ultimate treatment following their original publisher's demise. To wit, "Living City" became "Living Planar," "Living Greyhawk" evolved into "Blackmoor," and "Living Death" turned into "Fellowship of the White Star."
White Wolf's New World of Darkness is an Ultimate Spiritual Successor of the Old World of Darkness, created to tighten focus, tweak rules mechanics, standardize rules between different gamelines, and replace a metaplot continuity that in just a little over a decade had become as convoluted and incomprehensible as any comic book universe with a more ambiguous, optional, and largely more internally consistent one.
It's been confirmed that another White Wolf product, Exalted, is going to be given this treatment in the coming third edition, with the map redrawn and multiple new types of Exalt appearing. The fanbase immediatelyunderwent extremely hostile mitosis on whether this was a good thing.
Played straight twice: not only is Original Generation an attempt to blend all originals into one cohesive storyline, but it got a Continuity Reboot. Originally started on the Gameboy Advance, a Video Game Remake on the PlayStation 2 entitled Original Generations tweaked the storylines and certain character personalities to make more sense, while adding new scenarios, units and characters from other Super Robot Wars (even some from obscure titles, such as Great Battle IV). It's not as major a reboot as many other examples here, but it IS the Ultimate Universe for developer Banpresto.
The Batman Arkham Series is somewhat an example. The story is largely self-contained, and while there are references to previous Batman comic stories, they generally have the story weight of Mythology Gags.
The 2012 TMNT series uses aspects from many previous continuities. It's more or less got many of the 1987 show's plot elements, but has a tone that slowly becomes more in line with the 2003 series, as well as the show's use of Composite Characters and sometimes reworking the origins of particular villains (The Rat King and Mutagen Man being the most notable).
ThunderCats (2011), which functions as a darker, more dramatic take on the original ThunderCats, showing the more realistic aspects of the war between the cats and the lizards, as well as the culture of the main characters.