Inconsistencies between this and Wolverine and the X-men

To begin with, in this episode, Wolverine seems to remember Weapon X and recognises Sabertooth and the Professor.

Keep in mind, he doesn't actually call either by name and seems more concerned with escaping, though he does hear the Weapon X term and gets some of his memories back while knocked out.

Furthermore, the Professor is killed in this episode

Not really, pay attention to the scene where Deadpool and Omega Red arrive on the scene of his attack, "Prof" is still hanging on and Deadpool emphasizes as much "Well, he's alive, but I'm afraid he's gonna need some serious TLC!".

In the flashbacks of this short, we see Logan being captured by force outside a bar, given the adamantium treatment, being systematically mindwiped and reprogrammed as a killing machine, and escaping during the process...all of which is pretty much a faithful adaptation of the 'Weapon X' miniseries.

However a lot of this conflicts with what we see (or can surmise) from WatXM. We see Logan working for Team X alongside Victor Creed/Sabertooth (which is also true to the comics), but he already seems to have his claws. But, as per the Hulk vs. short, Logan escaped from Weapon X just after getting his claws so there's hardly a chance he carried out any missions in the interim, at the time when he was being treated like a lab rat by the Professor as per the short. Come to think of it, if Logan's memories were wiped after the adamantium process, then how does he not remember the mission against Christopher Nord, seeing as it should have been post-amnesia if he had his claws?

I made a timeline sorta explaining all this:

As near as I can figure, mind you this takes in account Hulk Vs. and the new Avengers cartoon as well, Logan's past in the Wolverine & X-Men universe is made up like:

World War II -- Works with Captain America, as seen in a prequel micro-ep of "The Avengers: Earth's Mightiest Heroes".

At some point, joins Professor Thorton's Weapon X team, taking on the same code name as the titular team, working with Victor Creed for years.

Some time into the years with Weapon X, meets and falls in love with Raven Darkholme. Seeing the more shifty and dark sides the team was willing to sink to. Decides to escape the HQ complex with Raven, but she gets away without him, though Logan soon manages to also escape offscreen.

Drowning his sorrows of missing the escape with Raven and no longer able to return to Weapon X, Logan leaves a Canada bar drunk, only to stumble into Professor Thorton whom "reacquires" him for Adamantium bonding. Logan's head is shaved and he's forced to under-go the procedure, all this is seen in the Hulk Vs. Wolverine portion of Hulk Vs.

Logan takes quite a long while to heal following the bonding process, bandaged in a medical tube, as seen in a Wolverine & The X-Men flashback. As additionally seen back in Hulk Vs., he finally awakens once his hair has grown all the way back out, chained in a dungeon as he discovers he now has claws that most painfully eject from his hands. Logan is put through mental engineering trials to ensure he can be controlled, eventually being put back on missions with the likes of Sabretooth, Deadpool, and Omega Red, all the while a clone-daughter of him is made via X-23.

(I presume one of these missions was to take out Uriko/Deathstrike's family, most probably by Logan's hands, prompting Uriko to seek vengeance against him alone by later joining Weapon X following Wolverine's last escape)

Logan's last mission is under the command of Sabretooth, where he's ordered to assassinate Maverick and his daughter, all the while control of his faculties is finally coming back to him (apparently without the memories of trying to escape with Raven and being abducted by Thorton). He eventually rebels against the mission, only to be knocked out.

Back in the perspective of what Hulk vs. shows, Logan is taken back to the Weapon X complex for his memories to be completely wiped in hopes of once again being controlled. However this time, he comes back to his complete senses and escapes the complex in a primal and furious rage, though now with a complete blank in regards to his memories. Much like the end of Origins: Wolverine with how he "awakens" into his new clean slate of a life, this is the equivalent point for him in this universe.

Journeys to Japan in running away from whatever he was just put through, soul searching and hoping to remember answers as to who he is. Logan meets Mariko Yashida and falls in love with her, though is shunned after she chooses the Silver Samurai, despite his victory in a battle of combat. He leaves Japan, returning to Canada.

Becoming a member of Department H, Logan embraces the iconic Wolverine costume in his missions for them, ultimately taking up one toughie in particular... taking down the incredible Hulk! This mission leads him to being found by the remaining members of Weapon X, including the now-recruited Deathstrike. Certain portions of his memories come back to him while initially knocked out by them, the earliest of which was the drunken night where Thorton abducted him, the Adamantium bonding process, a couple trials/missions, and his final escape. He subsequently defeats them, Deathstrike and Omega Red being killed by Hulk, whilst the Professor, Sabretooth, and apparently Deadpool barely survive.

(Considering the implying that Hulk ultimately won in his and Wolverine's fight, I like the notion that after this, either Xavier or Rogue found him 'near death' in the snow. If Rogue, then they could get to know each other well, perhaps with her nursing him back to health, before Xavier finds them and offers a place at his mansion. While Rogue goes, Logan stays to think it over, eventually choosing to leave behind Department H and come to Xavier's school)

Logan comes to the Xavier school, though due to Cyclops' intense jealousy, his stay is apparently only in the span of a few days to a couple weeks. Then... the explosion. Wolverine & The X-Men begins.

"The End of the Beginning", 'cause on May 13th, Superman Begins~!!

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