Rallen and Jeena may have managed to stop the Krawl invasion of the Nanairo Star System and forced them to retreat... but a new evil power has emerged and is leading a new assault on the galaxy. Unfortunately, the enemy made sure to make it more difficult this time by destroying all of Rallen's fossils and Spectrobes. Once again, it's up to Rallen and Jeena to excavate and train Spectrobes in order to defeat the Krawl menace threatening the star system.
Spectrobes: Beyond the Portals plays much like its predecessor with exploration, excavating fossils and battling as the central theme. But the game has been equipped with a 3D camera this time, making exploring a 360 degree experience.
The gameplay mechanics have stayed more or less intact since the previous game. The player will excavate various minerals and fossils using the stylus and the microphone and a plethora of different digging tools. Battles play out in real time, either with Rallen on the field, or in a separate battle screen with the Spectrobes.
New to this game are "Badges", which act as a form of achievements. Fulfilling certain criteria in the game will unlock them, such as defeating a certain number of enemies or unlocking all of the hidden mini-games.
Via WiFi and on a dedicated website players can battle against each other or exchange Spectrobes and items. It is also possible to trade Spectrobes between this game and the original game. Items and Spectrobes can also be added to the game using game cards with holes through which the touch-screen must be touched in a specific order.