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N, his sisters and his presumably deceased mother are all Zoroarks owned/fostered by Ghetsis.
What triggered N wanting to liberate Pokemon from humans was seeing his mother (a pokemon) abused (potentially killed) by his "father" Ghetsis. We know Ghetsis abuses N too, so that's why he obeys out of fear. But his end goal is to free all Pokemon and eventually defect from his father and Plasma when that goal is reached.
