Imagine Antagonists as members of factions, instead of a game mode in rotation

[Helios]

There's a lot of ways we could add more depth to antagonists, by taking them seriously. Understanding who they are, how they operate, and how with internal consistency we can change that around.
So as an example, instead of random jobs being changelings, changelings try to infiltrate a specific department. This could happen before the round (3 Changelings spawn in Botany), or during the round (3 Changelings show up with the uniforms and IDs of Quartermaster and 2 cargo techs, and try to take over the department)
Many main or side antagonists are capable of launching a ship. Abductors are an advanced civilization, whether they recognize Centcomm, or Centcomm recognizes them. Given their amount of gene editing, they could could have Frank Horrigan level Terror squads, or gene edited beasts of burden that can be traded to friends.
And yes, you could get a cult ship sent from a station where cult summoned Narsie, a spider or zombie ship, and give side antagonists a new direction or objective, but it's not just about that. To mirror the Cuban Missile Crisis, you could have a department of revolutionaries, who's objective isn't to convert the masses, but to obtain nuclear deterrence, so if sec attempts to raid their department and arrest everyone they can push the big red button and end it

[vect0r]

Like they wouldn’t press the big red button for the lolz.