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Yes, that part is hard. Just keep shooting them with the minigun (you should have researched it already by the time and upgraded your's cyborgs a little and have enough money to buy the miniguns, if not, spend little time with waiting for money & research in the menus). In first 2 encounters with them the MP's could suffice also, but after that - only minigun.
In some of the missions, you also can use flamethrower against them effectively - if you place your's cyborgs strategically, they (enemy) may move into a house, when they are after you, just approach the house carefully, and, if they don't come out then, carefully move into the house and start burning 'em :twisted: Just don't forget, they can shoot at you in the house too, just not that often like outside.
Also if there are enemy cyborgs from more than one company in the level (different head-colors), they may get on themselves first too, just let them until there is only small amount left. When they're after you again, start shooting them (minigun, of course).