[Nazo > Team Spectrum]: They've been missing for long enough that the capture spheres were still unknown to us at the time, correct? I suppose we could press Giovanni for more information on them.
[Nazo > Team Spectrum]: Fighting is the only thing strong against all of them, seeing as one is normal. Hiding away could be a number of things. A possible dark type?
[Nazo > Team Spectrum]: If the only known Mewtwo in this world before Giovanni was Karat, that could be a case of mistaken identity. Wouldn't be the first time Karat was mixed up with a villain by species.
[Nazo > Team Spectrum]: If one of the three is Giovanni, mixed up with Karat, the third is really only the second as far as spies go. It's possible they just didn't know about a third spy, but also possible that no such third existed at the time.