Team Aqua and Team Magma were still active as rival villain teams during the events of Pokémon Omega Ruby and Alpha Sapphire , but the games do not give them a big “afterward” storyline beyond that conflict. Their roles in Hoenn are focused on their opposing goals: Team Aqua wants to expand the sea, and Team Magma wants to expand the land, with Archie and Maxie leading those efforts.

What happened to them after

There isn’t a major canon update in Omega Ruby/Alpha Sapphire showing a brand-new postgame plan for either group. The story mainly treats them as still functioning organizations whose ambitions are stopped by the player, rather than teams that go on to a completely new phase immediately afterward.

In practice

  • Team Aqua continues to appear as Archie’s group, pushing its ocean-expansion goal.
  • Team Magma continues to appear as Maxie’s group, pushing its land-expansion goal.
  • Their conflict is framed as ongoing rivalry inside the Hoenn storyline, not as a settled “what they did next” epilogue.

Simple read

So the safest answer is: they didn’t get a clearly defined new post-ORAS activity in the games themselves; they were simply defeated/stopped and remain known as Hoenn’s rival villain teams.

Quick scoop: there’s no official, detailed “after the events” mission for either team in Omega Ruby /Alpha Sapphire —just their same old ocean-vs- land conflict.

TL;DR: Team Aqua and Team Magma were still operating during ORAS, but the games don’t spell out a separate long-term plan after the main story; they’re basically left as Hoenn’s recurring rival organizations.