She said "Something unexpected happened when they were struck by the attack intended for Deoxys... Deoxys has escaped, but it seems I have reaped something of equal value in return.", if I'm not mistaken. After saying that, she just smiled, said "Goodbye for ever, my dear Pokédex owners." and left.
By Team Rocket, maybe - maybe not. Archie said that the person who gave him the set of armor and sword was a person named Galactic, though he could only say "Gal" before disappearing. But from what Archie said, we can guess Sird is actually a member of Team Galactic. But nothing is official yet. o_o'
Personally, I think Mewtwo is just coldblooded.
Mew is better than Mettwo, but when I was smaller (12) I thought that Mew evolved into Mewtwo.
I guess they don't evolve from or to each other at all.
Of course Mewtwo was captured! What's all that nonsense about teleporting? It is attacking Sird along with Pokedex Owners one second and running away in fear second after? Does that make sense? Answer - not at all. Because of Deoxys battle it was very weak - also Sird's Ball didn't look like a normal Pokeball/Greatball/Ultraball whatever. What kind of ball uses such beam to do a long-distance Pokemon capture? Mewtwo was captured, and is now in Team Galactic filthy hands!