I'm quite aware of Mewtwo's origins, but I use the term "mutant" because that's definitely the concept behind it in the games. Something unnatural that's been changed from its original form. Man-made mutations, perhaps, but even so.
I just want a plot where a pokemon is going out of it's way to do something about the newcomers.
....honestly, one of the many, many other legendaries would fit the bill much better for this idea, in my opinion. Maybe not in your exact scenario, but there's PLENTY of "guardian"-type pokemon, most of them legendary, even, who may take issue with a lot of strange trainers trampling all over their territory. Celebi would be pretty near perfect for such a role, and it's a Johto legendary, even! But I frankly can't see Mewtwo as being one of them, or even caring about the newcomers, period.
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And deus ex machina means in regards to plot, not game mechanics. Having a god isn't the same as having a god appear to change things for no apparent reason. Greek plays were chock full of gods, often falling into ungodlike behaviors, but the cliché of the "god of the machine" only applied to the particular circumstance of a god suddenly appearing out of nowhere to fix things for no apparent reason. Which is what I'm getting at here.
I just want a plot where a pokemon is going out of it's way to do something about the newcomers.
....honestly, one of the many, many other legendaries would fit the bill much better for this idea, in my opinion. Maybe not in your exact scenario, but there's PLENTY of "guardian"-type pokemon, most of them legendary, even, who may take issue with a lot of strange trainers trampling all over their territory. Celebi would be pretty near perfect for such a role, and it's a Johto legendary, even! But I frankly can't see Mewtwo as being one of them, or even caring about the newcomers, period.