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Here's what works best:
1.Fight them in space, this will cause them to lose a great deal of biomass, making the swarm weaker as a whole.
2..Kill the leaders, it may not stop the swarm, but it slows them down considerably.
(if you have enough resources and/or hold out long enough for reinforcements you can win)
and if that fails
3. Exterminates: Forces them to lose bio mass, if you cause enough damage to the fleet as a whole with the above steps you can stop the swarm as a whole, forcing them into hibernation.