Fall of Metru Nui
For more details on this topic, see Bionicle Adventures.

[edit] The Great Shadow
18 Months Before the Great Cataclysm
Makuta secretly captures and impersonates Turaga Dume and takes his place.
Makuta creates the Karzahni plant monster; but the Karzahni is too powerful and ambitious so he creates a weaker version and calls it the Morbuzakh. He also hires Dark Hunters to help.
"Dume" orders all passages to and from Metru Nui sealed off. The Toa sent on these and other missions are killed one by one until only Lhikan is left.
Around 1 Year Before the Great Cataclysm
The Morbuzakh is unleashed and begins to kidnap Matoran and cause property damage. The rest of the population to evacuate towards the city's center.
Lhikan becomes suspicious of "Dume" and begins to investigate.
A Few Weeks Before the Great Cataclysm
Lhikan chooses six Matoran and gives them Toa stones. He is captured upon delivering the final one.
The Toa stones transform the Matoran into Toa Metru. Toa Vakama receives a vision telling him to find the Great Kanoka Disks.
Toa Metru search for the Matoran that know the Disks' locations, then for the Disks themselves.
Toa Metru destroy the Morbuzakh using the Great Disks.
Toa Metru face Krahka, waking a Tahtorak in the process.
Despite the Morbuzakh's defeat, Matoran continue to disappear.
The Great Cataclysm
"Dume" orders arrest of Toa Metru. Three are captured and locked up with a Turaga.
Imprisoned Toa Metru escape; join free ones. Turaga revealed to be Lhikan.
Great Spirit Mata Nui falls asleep, leading to the Great Cataclysm:
Metru Nui hit by earthquake and double eclipse, reducing the city to ruins. Quake also breaks many of the Archives' stasis tubes, freeing the Rahi inside.
On the planet's surface above Metru Nui, energized protodermis transforms a barren island into a lush tropical paradise.
Mount Valmai and the surrounding region breaks off of its landmass and rockets up to the surface, becoming the floating island known as Voya Nui. Turaga Jovan killed in the process.
The dome surrounding the Pit shatters, causing the sea to flood in. The waters mutate the inhabitants into water-breathers, keeping them from escaping outside the ocean.
Brotherhood of Makuta's corruption exposed worldwide.
Makuta transforms from his Dume form; absorbing the Dark Hunters into his body.
Toa Metru confront Makuta. Mask of Time created; lost in sea. Turaga Lhikan killed. Makuta sealed in solid protodermis.
Days After the Great Cataclysm
Toa Metru arrive at the newly transformed tropical island; name it Mata Nui