Complex sentence: Troops of the Federation alliance had set foot into Cardassian territory and the Dominion was seeking new allies, which they found in the Breen-confining the Cardassians to second class status.
Split into simpler sentences: Troops of the Federation alliance had set foot into Cardassian territory and the Dominion was seeking new allies. And they found them in the Breen confining the Cardassians to second class status.