Plot twist: When Vakama turned evil he stayed evil, but decided his rule was better served along side Matau.
So, Matau and Vakama hatched a plan to overthrow Roodaka and gain control of the rest of the Toa Hordika.
When they left for Metru Nui (after they reverted to Toa Metru) Vakama said he would return because he needed to find the Mask of Time.
He made a plan with Makuta to give Mata Nui enough time to almost die by holding the Toa Mata summoning stones hidden.
But, Takua found the stones and summoned them.
When the Toa where fighting Makuta, Matau was sent to activate the Bohrok.
Although once he did they captured him and the rest of Le-Koro was captured because of this.
That's why the Bohrok already did so much damage when the Toa came out of the Kini Nui.
Vakama also knew way too much about the Bohrok, Kranna and powers.
Vakama always used "visions" as a way to explain away why knew so much, but it was really because of his connections with Makuta.