I thought the Matrix hurt him because he was trying to siphon healing power from Dreadnought.
Side Note: I personally believe that all XT really needs an upgrade on is his healing; with his years of combat and life experience, coupled with his armor design and Bio-Rythmic Cannon he should be a match for about any foe, no matter how powerful. Besides I remember reading that XT received a tremendous power boost from just a simple intake of energy from the Kregen.
I believe the Black Orb was from the Kregen, after all XT was the only one who came the closest to defeating Anubis.
P.S. The Space/Time paradox was referring to when W'kar would meet up with Anubis.
I've a question, is there a possibility that this Grakken assault will weaken the Grakkens, provide a new battlefield for Chronos and the ACTF(Space). Also, will this allow a new enemy to rise, and will any of this lead to the unveiling of the Dark Being Darmon and/or the return of his crystal?
EDIT:Sorry if I'm asking too many questions
I believe the Matrix would make modifications to the Giant Unit more so than his Warrior Unit.(Seeing as how upgrades are in, instead of having powerful regular units)