In Advent Rising, you play as Gideon Wyeth, a rookie space pilot. Gideon has a loving fiancée and life smiles. That is, until mysterious aliens appear. Gideon and his brother, a hero space pilot, are invited to the historical greeting party. Though the aliens are friendly, they come with a warning about another, vicious race, known as "the Seekers", who have decided to exterminate the human race. Soon after, the Seekers invasion begins, and so does the actual game.

The game itself is a third person shooter with superpowers and a rudimentary melee fighting system. Alternatively, it's possible to switch to a first person perspective, although some abilities cannot be used in this view. Generally you just go around shooting aliens using a new kind of targeting system called flick-targeting. While on Xbox you select targets by tapping thumbsticks towards the foe you want to shoot, on PC this happens by scrolling the mouse wheel (although you can use the mouse for manual aiming and thus avoid scrolling through long list of enemies). You can also gain psychic powers to aid you in combat, ranging from lifting enemies into the air and slowing down time, to creating shields capable of deflecting attacks and smashing enemies with an electromagnetic pulse. These powers work like character upgrades, each one having five mastery levels. Jumping and melee fighting are also upgradeable. As part of the jumping mastery levels, for example, is dodging in slow motion. Just like weapons, in order to use powers they must first be equipped in at least one hand.

During gameplay, the HUD shows Gideon's remaining health, the power meter, weapons and powers currently in use, and the number of rounds in the weapon. At first, you must find Nano Aid stations in order to recover health, however once Gideon gains mastery over his health, it simply regenerates if you stay out of harm's way. The power meter decreases every time a power is used, and if it's depleted you must wait for a time before you have access to your powers again.

While Advent Rising is mainly a third person shooter, Gideon will have the chance to control the Scythe ATV, turrets and various alien ships. The game has four levels of difficulty (easy, normal, hard and ultra), and uses a checkpoint-based saving system.