Vehicle minigames turn the game into a vertically scrolling shooter, a-la Galaga, and you must grab weapon pickups to upgrade your weapons to take out the enemies. You'll encounter both ground and air enemies, with being ground attacks and the standard being your primary attack.
You can do this on Mission 2, Mission 5 (I did it on 5), Mission 6.
In order to get through these safely, keep the pointing forward, and keep tapping to continuously launch missiles and bullets. Obviously avoid enemy rockets (you can't shoot them all, some ignore bullets), and watch out so you don't crash into enemy planes/helicopters - especially at the bottom of the screen. The most important thing to note is: utilize checkpoints. If you get hit after a checkpoint, simply hit and load to reload the last save.