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The series X-Men: Evolution featured a diverse cast of complicated characters. A common staple of the series was whether a particular person had chosen their allegiances correctly, with several instances of a character switching teams.
As a whole, the New Mutants did not have a significant role in the series. They were added in the second season of the show to make the Xavier Institute seem more populated by having several students in the background, and primarily have supporting roles.
The Brotherhood of Mutants are a group of mutant criminals led by Magneto who oppose the X-Men throughout the series. In a flash-forward depicted in the series finale, the group's members reform and join S.H.I.E.L.D.
When the Brotherhood of Mutants fall out of Magneto's favor, he creates a new team. Though never named on-screen, they resemble the Acolytes, a team led by Magneto in the comics.