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Anyways, Neo TeamRocket are the Ultimo de Rockets. That means they're Giovanni's most trusted Rockets. But this isn't in the anime. I think in the Manga.
Neo Team Rocket is part of the TCG and the Manga series. They are the group of people that wear the masks and inhabit the Johto Region. I think the 4th Movie had one member of them in it.
I don't believe Giovanni is behind them in any way. Anyway, check the Manga section for more information on them.