Once again an evil madman has the world to ramson involving nuclear warheads, and it's up to one man (or two if playing with a friend) to fight and shoot his Goons over various locations to get to the madman's complex on an island in the middle of the ocean and stop him once and for all. In a homage to James Bond, S.P.Y. Special Project Y has a variety of game styles over various levels which need completing to complete your mission.

You start off flying a Jet-Pack over the ocean from a 3rd person perspective flying into the screen towards the island with the baddies coming towards you. You have a gun but can get icons to upgrade your gun. There are Hang-Gliders and a huge Helicopter to contend with as well before landing on the island and onto the next stage which the game then becomes a Beat -em-up. You view the action from the side as the game scrolls horizontally as you move from left to right. Baddies come at you from all sides and you kick or throw them. Baddies with guns will drop their weapons which you can collect and use before facing another boss who needs defeating to move on.

Other game styles played has you running into the screen from a 3rd person perspective shooting the baddies coming towards you. As well as various weapons, you can collect smart-bombs to kill all on screen. The last style of gameplay is a beat-em-up again with weapons but you must jump up various levels to get to the top. As the game progresses it mixes up each level with these game styles.