Ace Attorney 6 continues the investigation and courtroom of its predecessors, in which players take the role of the defense attorneys; Phoenix Wright, Apollo Justice, and Athena Cykes, and try to defend their clients. The game continues the 3D navigation introduced in Phoenix Wright: Ace Attorney − Dual Destinies, allowing players to navigate environments from various angles. Along with returning gameplay elements, such as the Mood Matrix introduced in Dual Destinies, the game introduces Spirit Medium Vision, in which the players are shown the memories of victims moment before their deaths and must find contradictions in their five senses to determine what really happened.

The story of Ace Attorney 6 once again focuses on defense attorney Phoenix Wright and his two understudies Apollo Justice and Athena Cykes. Phoenix gets reunited with his longtime friend and spirit medium companion, Maya Fey, while visiting the island of Kurain, where lawyers are deemed unnecessary as spirit mediums are able to conjure up visions of a victim's memories moments before death. As ever, Phoenix and Maya seek to prove out that even a supposedly definitive method of convicting defendants has its own contradictions, while Apollo and Athena stay back home and have their own set of cases to deal with. Trucy Wright, Phoenix's daughter, becomes Apollo's defendant after a death occurs during one of her shows.