The Brotherhood of Mutants In Animation - A Retrospective
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Though they were never called the Brotherhood, several members of the team appeared in the early seasons of X-Men: TAS. Blob, Avalanche, Pyro and Mystique appeared in a combined five episodes of the first season. That's more than Magneto, but quantity does not guarantee quality.
Pyro, Avalanche and Blob are essentially filler villains. They only exist to get whooped with great frequency. They are established as non-threats the moment Pyro and Avalanche get summarily whooped by Rogue in a bar brawl.
The closest these tryptich ever get to being legitimate villains is when Blob hits Storm in the head with a tub of ice cream.
You didn't misread that: Blob. Storm. Tub of ice cream. How could anyone take them seriously?
No one ever refers to this assemblage as "The Brotherhood of Evil Mutants." (Probably because that was an obviously outdated name by the 1990s.) Also, this teams patterns itself more after the Freedom Fighters iteration of the team with Mystique as the leader instead of Magneto.
In fact, Magneto never associates with this Brotherhood, though Apocalypse occasionally gives Mystique orders.
The group appeared once more in season two and never again afterward. The creators had already devalued the characters too much as legitimate threats. They were essentially a villainous comedy troupe, except... not funny.
Lone members made the odd appearance. Mystique appeared in the "Beyond Good and Evil" series and "Bloodlines" and was used well in both. Perpetual member Toad had a pointless role in "Secrets not Long Buried" and he was still wearing that damn collar.
Former comic Brotherhood members Scarlet Witch and Quicksilver appear in X-Men: TAS but never as villains.
In summation, the Brotherhood members of X-Men: TAS still didn't approach anything resembling respectable. They would have to wait one more series for that.