Spectrobes: Beyond the Portals carries on the tale of Naniro Planetary Patrollers Rallen and Jeena. In their adventures to fend off the evil Krawl invasion of the Nanairo system. In order to protect the galaxy, Rallen, a renegade macho-wannabe NPP officer, will unearth, awaken, evolve and battle "spectrobes." These creatures can be tamed and contained in Rallen's "Prizmod" device and used to battle the Krawl forces in 3(you 2 Spectrobes) vs. 2-3 enemy(krawl) three-dimensional battles and are leveled up in typical role playing game fashion with battle progress, but also with minerals dug up from the "Excavation" mini-game. There is also exp. points that are used for your excavation (it unlocks better tools for you to use).
Spectrobes: Beyond the Portals gets its title from aspects of the story, as Rallen and Jeena are forced to pursue their kidnapped comrade, Aldous, who played a critical role in 2007's Spectrobes, Portals also play a significant role in the final stage of Beyond the Portals, as Rallen hunts down his most sought after enemy, Krux, the leader and commander of the Krawl horde.
Not unlike the first game, Spectrobes allows the use of Input Cards to unlock various items and spectrobe creatures to battle with; by placing these plastic cards over the Nintendo DS's touch screen, you're able to unlock the respective item/monster by sequentially tapping specific points on the screen. New and rare spectrobes, including the new "dark spectrobes" can be unlocked using these Input Cards.
Now just like last time the Krawl are attacking the system and it is up to Rallen to save the galaxy with the help of the spectrobes and the rest of the police force. This time though Aldous is kidnapped (as stated above) by the High Krawl and now you discover that you have to fight these High Krawl before they destroy the towers located on each planet that help keep the Krawl at bay. However you fail at doing this because of the High Krawl leader (not the main boss).