Deus Ex GO comprises seven chapters, with a varying number of levels per chapter. There are 54 levels in total. In addition to these puzzles, new puzzles were released on a weekly basis.
Adam Jensen is sent by Jim Miller to billionaire Sasha Novak's mansion to save him from terrorists. As Jensen overcomes the terrorists in the mansion, he discovers that Novak is being held in the vault area. Jensen and Alex Vega determine that the terrorists are unusually well funded; Vega discovers that the terrorists were funded by an unknown group at Kostbar Bank, Switzerland. Jensen finds Novak, but Novak is gravely wounded by a guard. Jensen kills the guard, and quickly calls an ambulance. Miller and Jensen agree that Jensen should investigate Kostbar Bank for the group funding the terrorists.
After Jensen arrives, Vega tells him that Novak owned a security firm known as Ironflank. As Jensen continues to move through the bank, Jensen discovers that the guards inside as members of Ironflank. Miller tells Jensen to stand down, but Vega says Ironflank won't share the information they find. Jensen decides to continue to evade the Ironflank soldiers and attempt to find the information himself. He discovers that Ironflank funded the terrorists who tried to kill Novak. Jensen goes to the Ironflank HQ for more answers.
Upon arriving at the Ironflank HQ, Jensen finds out that Ironflank is a testbed for a government-funded military program run by Novak. Upon further investigation, Jensen finds out that Novak tried to sell his research to Chinese corporations, leading him to believe that someone wanted him dead for this action. While inside the HQ, Jensen accesses the Ironflank bunker; as he does so, Miller contacts Jensen, informing him that he knows that he is within the Ironflank HQ. Jensen tells him what Ironflank is doing, which causes Miller to reluctantly agree to let Jensen continue his investigation. Jensen then passes through a passageway that leads to the Ironflank bunker.
As Jensen moves through the bunker, Miller tells him that the ambulance carrying Novak's body never made it to the hospital, and that a ruse had been put in play. Shortly after, Novak appears, holding a briefcase in an elevator. Novak turns on the bunker's alert and escapes to a secret lab. Vega tries to warn Jensen of the danger, but her message is too corrupted from a communications jam to explain more than that. Jensen finds a computer in the bunker that tells the code to a secret lab - 0451. Jensen decides to investigate the secret lab, located in the basement. He finds the entrance, enters the code, and uses the elevator inside to descend into the lab.
Upon entering the lab, the communications jam is removed. Jensen tells Vega that Novak's military program was about weaponizing augmentations. Miller then contacts Jensen, and informs him that Novak is escaping through tunnels near the lab. Jensen is tasked with defeating Novak there before he escapes. Jensen contacts Novak and tells him he won't escape. Novak says that he had no choice but to sell government secrets on the black market, because his investors had bailed after the Aug Incident. Novak also reveals that he had to disappear for safety reasons.
Jensen eventually finds Novak, who is about to escape. Miller orders Jensen to kill Novak to prevent his research from falling into the wrong hands. Vega suggests incapacitating him so that the world will know the truth of his weapons research. If Novak is killed, Picus will praise Novak's contributions to military research and note that his research will likely be lost, while falsely blaming Purity First on Novak's assassination. If Novak is arrested, Picus will report that TF29 had uncovered Novak's plans in making military-grade augmentations, suggesting that Novak's research will not be lost.
Deus Ex GO is a turn-based puzzle game. The aim is to move Jensen from the starting point of a level to the end point (marked with a circle) while avoiding being killed by enemies. Enemies will move directly after the players turn. The player must take an action during every turn, meaning that Jensen cannot stay on the same spot for two turns. Jensen can take out enemies by moving to the same location as them, as long as he does not approach them from the front. Later in the game, Jensen gains access to bionic handgun and is able to take out enemies from afar (each shot consumes a biocell). If an enemy and Jensen walk onto a certain spot on the same turn, Jensen will be killed.
Hacking consoles can be found in various levels that allow turrets and red tiles which block movement to be hacked. The turrets become allied with the player when hacked, and shoot any enemies that enter its line of sight. The red, impassible tiles turn to regular tiles and can be walked over once hacked. Later levels feature similar tiles that allow for movement along certain paths, but not others. Hacking them rotates the tile to open up new pathways. In levels with drones, the drones can be "hacked" so that they turn to face a different direction. To hack an object, a line must be drawn from the hacking console to the object. Lines cannot be drawn over red tiles and enemies surrounded by red hexagons.
Blue triangular pick-ups that act as biocells allow Jensen to turn invisible for two turns by activating the Glass-Shield Cloaking System. He becomes invisible to both human enemies and robots. However, if an enemy walks into him, he will be killed even when cloaked. In later levels, this pick-up can also be used to remote hack consoles and even act as ammo for protagonist's handgun so he can take out enemies from distance.
Enemies in Deus Ex GO include human guards, bots, turrets, and drones. Each enemy type has different behavior so different tactics need to be employed to evade them. Guards either look in a single direction, or turn periodically to look in multiple directions. If Jensen enters their line of sight, they will begin to pursue him. They also activate the Titan Shield to protect themselves and cannot be attacked until they return to their original position.
Turrets are by default hostile to Jensen. They shoot and kill him instantly once he enters their line of sight. In order to walk past them without being killed, Jensen must either hack them or use Cloak. Hacked turrets can be exploited by Jensen to kill his enemies.
There are two bot types in the game: one is a large patrolling bot and the other is a small stationary one. Both bots only attack Jensen when he is in the spot directly in front of them.
Drones hover in the air and, like the small bots, remain stationary. Drones can attack Jensen from any amount of spaces away once he is in their line of sight. Once the drone spots Jensen, a red hexagon appears in that location and the drone begins to shoot it. This will kill Jensen if he stays on the spot, as well as any enemy that happens to walk over it when the drone is shooting.
Drones and turrets are invulnerable and cannot be destroyed by the player.
The "Mastermind" status is awarded to players who complete a level in a certain number of actions. These actions include steps taken and times an object is hacked. The maximum number of actions that can be performed to get Mastermind is displayed on the bottom left hand side of the screen. The number of actions currently taken is displayed beside it.
Achievements are awarded for each chapter if Mastermind status is unlocked for every level in that chapter.
- Based on the appearance of Miller and Alex Vega as in-game characters, the story in Deus Ex GO would be compatible with a chronological setting that is sometime after Deus Ex Universe: Children's Crusade. However, the events in Deus Ex GO are not referenced in any other Deus Ex media.
- The story's chronological relationship with Deus Ex: Mankind Divided is unspecified. However, the gameplay of Deus Ex GO depicts Adam Jensen with Remote Hacking and the P.E.P.S. augmentation, which, in the narrative of the series, were not available to Jensen until the events of Mankind Divided.
- At the release of Deus Ex: Mankind Divided, up to five Praxis Kits usable in Mankind Divided could be unlocked by playing Deus Ex GO. Two were awarded for completing the game, one for clearing all levels with Mastermind status, and another two for completing two sets of weekly puzzles.