Cortez last seen betraying Magneto is serving Apocalypse since his rescue from Asteroid M. Cortez is basically trying to find a suitable mutant to serve as Apocalypse's vessel since his physical form must have been destroyed when all the psychics sent him away into the astral plane. Jubilee was captured and almost made into a 'sacrifice' until the last moment. Although the temple was on the verge of collapse, the decision to not help Cortez paved the way for Apocalypse's return. Cortez without another mutant to offer was 'rewarded' by being taken by Apocalypse as the vessel and Cortez was sent to the astral plane in his place.
Had this series not been canceled, it would've been very interesting to see what sort of problems Apocalypse would've been to the X-Men.