The Toa Metru are nearly powerless after their defeat of the Morbuzalch but they cannot rest. Instead they must venture underground to save the city of Metru Nui's Archives. The Archives contain the history of the city. The Matorun and even the Toa. However, a flood has allowed all kinds of creatures that are normally kept in Stasis to escape and now the Toa must battle them to survive.

The guardians of Mata Nui learn of the six heroes who played the same role in the lost city of Metru Nui from which the people of Mata Nui came as the ancient warriors try to solve a series of disappearances and cope with a dangerously destructive plant.

Driven from Metru Nui by an earthquake, the six Toa Metru must protect their cargo of six sleeping Matoran, and set out on a perilous journey to find a new island home.

The struggle between good and evil continues in the darkness of the ocean depths.

Six Matoran travel to a mysterious island to rescue the Toa Nuva from monsters called the Piraka.

The six new heroes, the Toa Inika, have arrived on Voya Nui in search of the missing Toa Nuva, but what they find instead is the Matoran resistance fighting to free themselves from the Piraka. But when four of the Piraka steal the power of the mighty Brutaka, the Toa must fight for their lives.