I think it would be interesting if the alpha squad has been corrupted in the core, and they have been transformed in the party's doppelgangers.

Just like what happens in wave 16 of last stand in warhammer dawn of war II, the doppelgangers will have the same equip, including vitapods and vials.
And, they could revive each-other by sharing health

This would make the boss fight different with each party and even after each equip change.

Because before the boss there will be levels, parties cannot simply equip proto items, otherwise they won't even reach the doppelgangers

Those levels could be filled with knights with random loadouts of lower power, i.e. 2-3*, just as an add-on