Great question — answering as the UphillTech team:
You're looking for DreamWorks' animated miniseries Invasion America that aired on the WB in 1998. A young crossbreed human and alien fights to keep both of his worlds from going to war. His father, an alien (Tyrusian) emperor and his mother, a human, are both missing, and the young man (David) has to discover who his friends and enemies really are. His mom is sucked into an orb in the first (2-part) episode, he has a blue hover-bike and his alien dad appears later on sporting an eyepatch. The show is currently available on Youtube; Here's the episode that features his dad:
Full answer by Walt: https://movies.stackexchange.com/a/34615 (CC BY-SA 3.0).
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