Mewtwo makes a reappearance in Raids, sporting a very extra suit of power-limiting armor. Compared to OG Mewtwo, Armored Mewtwo has lower Attack, higher Defense, and a movepool tailored to strike at its counters' weaknesses. While OG Mewtwo (T5) is duoable, Armored Mewtwo is a trio at minimum, even with Fog.
As it currently stands, Armored Mewtwo is not very relevant for PvE. Its movepool is great, but it has a Base Attack of 182. For reference, OG Mewtwo has a Base Attack of 300. Still, Armored Mewtwo does share Candy with OG Mewtwo, and that's a good enough reason to want to raid it.
Minimum viable levels assume Best Friends, No Weather.
Italics indicate a Legacy move.
Meet Giratina (Origin, not Altered). It's the single best counter to Armored Mewtwo, not being weak to any of its moves. Against Earthquake, it's the only viable counter. Shadow Ball Mewtwo comes close enough that a couple of Level 40 Shadow Ball Mewtwos won't kill your run, given that you have enough Giratinas to do the bulk of the heavy lifting.
Legacy Gengar joins Giratina as a viable counter against Rock Slide. Level 40 Shadow Ball Mewtwo and Bite/Crunch Tyranitar are close enough to trio-viable performance that, again, a few of them won't kill your run if you have enough Gengars and Giratinas to carry most of the fight.
1Tyranitar is only trio-viable against Confusion/Future Sight; against Iron Tail, Tyranitar is a little too slow to be trio-viable on its own. With enough Giratinas, though, a trio using some Tyranitars is still possible.
Feint Attack/Foul Play Weavile and Shadow Ball Mewtwo are close enough to trio-viable performance that a few of them won't kill your run, provided you have enough Giratinas.
Legacy Gengar and Giratina have a field day against Dynamic Punch, with their Ghost-typing providing immunity-tier resistance to Fighting.
1Deoxys-Attack is trio-viable against Dynamic Punch on paper, but it dies 66-70 times. If you have one powered up, feel free to use it, but it is very taxing on Revives, and on slower devices it may not be viable at all due to how much time Reviving will take.
At Level 40, Shadow Ball Mewtwo, Legacy Shadow Claw/Shadow Ball Haunter, and Shadow Claw/Shadow Ball Banette are close enough to trio-viable performance that you can still win with a few of them slotted in, provided you have enough Gengars and Giratinas.