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Rift opens somewhere in Gotham that brings about omega red shortly before Braniac shrinks gotham into a bottle while Batman is away on a jla mission. The rest of Gotham's usual citizens and denizens are there.

Can anything stop him from taking over the city and cause mass slaughter?

Villian wize it would possibly be Clayface.
Or Solomon Grundy at Batman levels maybe?
The Corrosive Man might be able to due something if He isn't affected by the Death Spores.

good points