Although some key events occurred prior to the events of the original series as well as in between the original series and Alien Force, the timeline follows the canon timeline more or less until Season 2 of Alien Force. Most events from the canon timeline beyond this point either did not occur or occurred differently.
As was implied (but not followed up on later) in War of the Worlds: Part 2, the Omnitrix sending out a genetic wave to hybridize the Highbreed caused its main playlist to reset, giving Ben a completely new set of aliens and locking all the aliens he had previously unlocked.
Kevin's car was also destroyed, and he bought a brand new car at the auto show he left to attend at the end of the episode.
In the canon timeline, both Patrick[DM 1] and Cyrus' factions were stated to be of the line that directly flowed from the Forever Knights' formation (albeit at different times during the series' production). In Timeline 1 of Earth-50, it is unknown if this is true for either faction and it is unlikely that it will be explored.
Ben retired at the age of 10 instead of 11.
Alien X (and by extension, Celestialsapiens in general) veers much closer to his portrayal in Alien Force and Ultimate Alien, whereby:
Two out of three of his personalities need to agree in order to perform an action instead of all three.
Way Big's cosmic ray attack is executed by crossing his arms in an "L" shape, with his right forearm vertical and left forearm horizontal in front of it and the thumb edge of his hands facing his body, unlike in Omniverse, where he crossed his arms in an "X" shape.
Way Big does not have enhanced speed.
Like in Ultimate Alien, Mr. Baumann is on friendly terms with Ben and is not neighbors with him, but like in Omniverse, they started on bad terms and only grew to like each other as time went on.
Kevin needs a lot of whatever he copies in order to use his matter absorption powers, unlike in Omniverse where small amounts of material were sufficient.
In the canon timeline, Ben and Vilgax had an encounter when the former was 11. In Timeline 1 of Earth-50, the two have not met since Secret of the Omnitrix.
Celestialsapiens spend most of their time debating and do not partake in other matters such as changing the art style of the universe, as was established in Omniverse.
In the canon timeline, Manny was born a human and was later given Tetramand DNA by the Rooters. In Timeline 1 of Earth-50, he had no involvement with the Rooters and is a natural human/Tetramand hybrid with Plumber parents, namely a human father and Tetramand mother. The latter died when he was a baby, and the former was killed in action.
The Omnitrix symbols being positioned randomly on the aliens in the original series was the result of a feature that allowed for easy access to the symbols being turned off. Said feature was activated upon the Omnitrix's recalibration in Alien Force, explaining why the symbols were on the aliens' chests.
It should be noted that this feature excludes a few aliens as it would hinder their abilities in some way.
The Earth and intergalactic versions of the Plumbers were originally two separate organizations with very similar purposes, with the latter formerly being known as Liberation.
Sometime in the early to mid-20th century, they were inspired by the Earth Plumbers to change their name, and the two organizations became partners and began sharing resources. Despite this, the Earth Plumbers remained focused on Earth for the most part and only interacted with the intergalactic Plumbers when necessary.
After Vilgax's defeat by Max and Phil in the 1970s and the subsequent disbandment of the majority of the Earth Plumbers, the remaining Earth Plumbers began aiding the intergalactic Plumbers on missions in space.
It was not until after Ben's defeat of Vilgax in Secret of the Omnitrix that the two organizations properly merged into one.
Devin existed. However, he died when Kevin was four instead of five.[DM 2]
In the canon timeline, Max has been married more than once.[DM 4] In Timeline 1 of Earth-50, he has only been married once, to Verdona.
Max retired from the Plumbers at the age of 52 instead of his late fifties.[DM 4]
Petropia remains destroyed and Sugilite is still deceased.
Chromastone cannot fly and is much more resilient than his canon equivalent.
Contrary to what Dwayne McDuffie confirmed[DM 5], the flashback in ...Nor Iron Bars a Cage was the first time Kevin 11 reverted to human.
Kevin did not have any girlfriends prior to Alien Force.[DM 6]
The 5.22-year time period in which Sheelane sheds her skin is brought forward by one year.
In the canon timeline, Galvan Prime/Galvan Mark II was portrayed as being somewhat city-like in Alien Force and Ultimate Alien, having many skyscrapers and buildings, while it looked more natural in Omniverse. Both of these renditions are kept in some way, with the former being what Galvan Prime was originally and the latter being what Galvan Mark II is like after the original planet was destroyed by the Highbreed.
February: Season 1 of Alien Force (until All That Glitters) occurs.
March: The remaining episodes of Season 1 of Alien Force occur.
April: Season 2 of Alien Force (until Pet Project) occurs.
The remaining episodes of Season 2 of Alien Force occur.
The Omnitrix resets at the end of War of the Worlds: Part 2, giving Ben a new roster, consisting of Antigravitesla, Heavysplitter, Lodestar, Plantapocalypse, Porturtle, Purebred, Rock Bottom, Sparkhenge, Squidstrictor and Thriller Whale.
Kevin buys a new car after his old one was destroyed in War of the Worlds: Part 2.
Max begins training the Plumbers' Helpers.
News of Ben and his team's triumph over the Highbreed spreads throughout the galaxy.
June: While on a mission to deliver the Tiffin to Jarett of the Pantophage, Ben unlocks Rath.