#really fun question

Hi @thedragonmissionary! I’m so glad you enjoy my answers, it makes my day to hear that. :) Thank you so much for the holiday wishes, and I hope you had a wonderful Easter. 

As for your question, I’m willing to bet that the practical, real-world reason Mewtwo makes everyone forget the situations he’s in is because it relieves the Pokemon franchise from having to keep continuity with Ash’s encounters with Mewtwo. The endings of Mewtwo Strikes Back/Mewtwo Strikes Back Evolution and Mewtwo Returns could make for a thorny continuity issue with the rest of the anime. If Ash learns the lesson that all life is precious, would he start to have misgivings about battling Pokemon when the sport can cause so much pain? Having met Mewtwo, would there be any repercussions for Ash the next time he faces off against Team Rocket? If Mewtwo didn’t make Giovanni forget him at the end of Mewtwo Returns, would Gio still be obsessed with finding him? How would that affect Team Rocket's goals? Does Ash dying have any lasting impact on him? Etc. While I personally would love to see these kinds of scenarios play out, I also understand that it makes creating a coherent continuity that lines up with the release of the games, merchandise, etc., very tricky for such a multi-faceted and enormous international company like The Pokemon Company.

But creatively, that’s no fun. In-universe, I think there’s a way to spin it to make sense with Mewtwo’s character arc and personality. Wiping the memories of those involved with him is a way for Mewtwo to 1) spare his victims from some trauma, 2) ensure his safety and secrecy, and 3) spare himself some guilt. 

1. Wiping everyone’s minds is a way to spare Ash the memory of having been killed/turned to stone, Nurse Joy from any lingering memories of having been kidnapped, brainwashed and enslaved, the trainers’ Pokemon from having fought a death battle against their brethren, and otherwise remove all other traumas that befell those involved in the New Island incident. In this way, I think inducing amnesia in his victims is seen by Mewtwo as a small act of mercy.

2. Making people forget him also ensures Mewtwo and his clones’ safety. If nobody remembers you, they can’t come after you, right? Ash may have turned out to be a good human, but Mewtwo may not be able to count on the other trainers to keep his and his clones’ identities a secret. Mewtwo wisely wipes the minds of Giovanni and the other Team Rocket agents on Mt. Quena, a nonviolent way to ensure that his worst enemy will not come after him or his clones again. 

3. And finally--and this is really getting into headcanon territory--I think Mewtwo makes everyone forget him because it allows him to save face and lessens his guilt. You can’t screw up if nobody remembers you screwed up, amirite? As you’ve noted, Mewtwo tends to wipe people’s memories when a situation goes bad. On New Island, Mewtwo is proven completely wrong by a human child--the progeny of his sworn enemy, humanity--when Ash sacrifices his own life to stop the fighting. Well, they can’t remember how much the strongest Pokemon in the world screwed up if he wipes their minds! And perhaps Mewtwo can sleep at night knowing that he “fixed” his mistake. 

Then after the events on Mt. Quena, Mewtwo prepares to wipe the minds of everyone--his own clones included. He argues that this is for the safety of the clones and the healing spring...but in doing so, it’s implied that he’s going to make the clones forget what they are and where they come from. Perhaps Mewtwo feels guilty having made them, committing the same sin he feels his creators did when they made him? Maybe he feels guilty for having put his clones through so much misery, that they’d be better off not remembering him or where they’re from? (Maybe all of the above?) Wiping their minds would spare them some difficult memories, and it would lessen the guilt that Mewtwo feels for putting them through so much.

Then Meowth and Brock make a good point.

Meowth: “It’s only natural to wonder about who and where you came from, and someday these little ones are going to want some answers. Only there won’t be any… Not if you’re going to make everybody forget! So what if their parents were clones? They’re all living creatures. They deserve to live, and they deserve to know about themselves just as much as you or me or anybody does.”

Brock: “And just forgetting things doesn’t change the fact that they happened.”

--Mewtwo Returns (2000) [English]

I think it’s here that Mewtwo realizes he’s been wrong to feel ashamed and guilty, and that he’s been projecting that shame and guilt onto his clones. None of them should feel ashamed for being “unnatural” beings, and wiping everyone’s minds of what’s happened doesn’t “fix” anything. There’s nothing to fix; only to learn from.

Mewtwo: “If we are to look to the future as other Pokemon do, we must also be able to look to the past. The shame of that past is not ours. It belongs to those who used our past to set us apart.”

Ironically, Mewtwo is one of those individuals who used their past to set them apart from others. I take this quote as Mewtwo realizing that any guilt he has over his past is for him and him alone to bear, and the past is something to be learned from, not run from. 

Hi akagi27!

Thank you so much for your kind comment! I’m so glad to hear that you enjoy my Mewtwo content. It’s always great to hear from people who also like Mewtwo’s story. As for your question…

Hmm…what would have happened in Mewtwo Returns had Ash not been present? That’s an interesting thought experiment. In the movie, Mewtwo gives himself up to Team Rocket in order to save his clones. This involves being tortured and/or brainwashed by those two machines, with Giovanni saying that he will have Mewtwo head his army to take over the world. In a version where Ash, Brock and Misty are not present, I imagine one of two things could happen: Mewtwo, preferring to die rather than submit to Giovanni and not having anyone to help him to the spring, would perish in his efforts to free himself. 

In another scenario, Mewtwo would be doomed to become Giovanni’s slave, this time without his will or mind. (The nature of his servitude depends on how you interpret what those machines are actually doing to Mewtwo.) However, Mewtwo is strong, and Giovanni has a habit of underestimating him. Perhaps he would free himself from Team Rocket once again, maybe even at the hands of Ash & Co. should they face off with Giovanni at some point.