Each zone has its own Boss. The following is a list of zones and the Bosses which are featured in each:

Drycreek Plaza: M1 Tank
Garland Park: Hind D
Garland Technology Center: Tiger and Edge (URDA Special Agents)
Geyser 1: Derrick Lynch (URDA Leader)
Grassmarket Street: A-0940
Belforte Hotel: Jared Hunter (New Leader) on Jetpack
Crimson Sea: Jared Hunter (New Leader) on Speedboat

Note: The appearance of Derrick Lynch has changed greatly from the arcade version. He now has darker skin, a different uniform, and looks more menacing. His main weapon has changed in design, but it still fires like his shotgun did in the arcade.