Macross 2036 is a horizontally scrolling shooter set in the universe of the Macross anime series. The player takes control of one of the series' minor characters, the female pilot Mylene Jenius, who navigates the space fighter Veritech, fighting against ships and robotic soldiers of the alien Zentradi race. The player-controlled space ship is equipped with a vulcan gun (which can be upgraded with power-ups) and bombs, which are released simultaneously. Another button controls a special weapon, which the player can purchase for points (awarded for defeating enemies) between stages.
The game's stand-out feature are separate boss battles which usually occur after a "regular" boss battle that concludes a flying level. After that battle, the Veritech automatically transforms into a giant mecha called Battroid, and fights a boss enemy one-on-one. The mecha fires automatically, and the player only controls its altitude and the angle of the shot. Anime-style cutscenes advance the plot between missions.