The gateway guns allow you to place two gateways on the walls, floors and ceilings of the lab so that when you pass through one you emerge out of the other. As progress is made through the game different types of gateway gun are introduced with different effects. After the basic gun, you acquire a gun that creates two gateways of different sizes, passing through one way shrinks Ed to half his size and the other way makes Ed grow to twice his size. Then you find a gun where one gateway doesn't just connect to the others location but also its time, allowing Ed to travel back in time and encounter earlier versions of himself. Finally, the last gun manipulates gravity so passing through allows Ed to walk along walls and on ceilings.

Gateways takes place on a single sprawling map rammed with puzzles and challenges. As power ups are acquired more and more of the map opens up containing more power ups and secrets. In addition to the gateway guns Ed will also find a torch letting him light up the darker areas of the map and a mirror which can be used to deflect lasers.

A sophisticated help system helps Ed along throughout the game. Every puzzle has a help point next to it where Ed can use power orbs to find out if the puzzle can be solved using his current power ups and abilities. If it can be solved and you're still stumped then spending more power orbs will provide you with the solution.