The Utrom Shredder somehow came into possession of the Heart and used it to control the mystics. Although it appeared that the mystics were loyal to Ch'rell, attacking the turtles in Return to New York, Part 2, it was later revealed (in Fathers and Sons) that they were disgusted by their servitude; thus, they hatched a plot to resurrect their master by using an invisible bone demon to gather his helmet, gauntlet and body from the "Ninja Tribunal". The demon was defeated by Master Splinter and the Ancient One, and it is unknown if the mystics made any further attempts to free themselves, but their mistreatment at the hands of Karai (according to them, Shredder treated them fairly at least) reignited their desire to return to their true master.
To this end, the mystics tricked the E.P.F. into stealing the artifact and destroying it, finally freeing them from the Foot's control. They then set out to revive their master.