The game revolves around a cooperative mindset, with players playing off each others different skill sets. Each character has a distinct set of abilities, with Captain Kirk being a more typical shooter, armed with a phaser with a stun setting, and Commander Spock, a more stealth based character armed with a couple of abilities as well as a gun with a freeze setting. As the player plays through the game, they gain experience by scanning objects, hacking and discovering audio logs. Experience is used to unlock additional abilities for their respective weapons. The tricorder offers many shooting options and the characters have the ability to rewire turrets and hack flying drones. The two characters can help each other out by boosting shields and weapons.
Next to the corridor-based shooting gameplay, there is a space battle with turrets and many platforming sections. Certain stages are set in space, where characters need to dodge debris and a single level contains underwater sections.