The game focuses on action and exploration, and features over 60 items and power-ups. The gameplay borrows elements from classic games such as Metroid, Contra, Blaster Master, and Bionic Commando, among others.
Axiom Verge is a side-scroller action-adventure game where the player controls Trace, a scientist who, after suffering a crippling injury, wakes up in an ancient and high-tech world of Sudra. Elsenova, a giant war machine from the original Sudran civilization, asks Trace to help stop Athetos, a mad scientist who destroyed civilization before.
As the player progresses through the game, he learns secrets about himself and Athetos and recalls memories. Trace recalls that the explosion originally crippled him but, it enable a new perspective and a new revolutionary take on the laws of physics. The scientific community scorned him and started to call him "Athetos", meaning "without place". Athetos then discovers Sudra, using their technology to repair his body and found a further more civilized world beyond it. After failed diplomacy, Athetos used a biological weapon to exterminate the more advanced civilization and brought back the technology to take it to Earth. Trace (the player) learns that he is a clone from Athetos first days on Sudra.
After discovering the truth, Trace works together with Elsenova and the Rusalki against Athetos. After Elsenova kills Athetos, Trace is sent back to point in time when the lab incident occured but, this time, his history was altered so he was not injured. He develops an obsessing with returning to Sudra and starts researching like Athetos.