Gameplay in Beyond the Portals functions similarly to that of its predecessor. Players predominantly control Rallen in the field, although from time to time, they will be able to control Jeena to solve puzzles. Five planets of the Nanairo Star System, from the first game are accessible once more. At certain points in the game, portals will open that will allow the player to travel to different star systems. There are a total of ten planets and three portals spread out over four star systems. During normal gameplay, the player is given the option to play a mini-game, flying the Patrol Cruiser, whilst dodging asteroids, in order to travel through a portal that links to another star system.