At the end of every level, you face a boss. Before a boss begins, a screen will show up telling you the weak-points of said boss. Successfully defeating a boss takes you to the item shop, where you can buy items to power up your robot, and then you proceed to the next level.
The major difference between ExZeus and Counter Force is that you are able to freely point and shoot enemies with the Wii Remote using an additional lock-on mechanic. The game also features a two-player mode, where one player holds the Nunchuck and the other holds the Wii Remote, which uses a modified control scheme from the original ExZeus .