I can remember only a few things regarding the show, as it was long ago, and probably late at night. However, I do remember it had to be a series, because it ended on a cliffhanger, and it was animated, and it was on the T.V. (Edit: I had an antenna, not cable or satellite at the time, so I'm thinking it was on Fox or ABC or CBS or PBS or sommat) sometime between the late 90's and the early 2000's.
I remember the protagonist had something of a metallic/robotic hand, which he used as something of a key to access alien devices and converse with a motorcycle he received during the episode I watched.
The motorcycle looked like an antique out of Indiana Jones and the Last Crusade, and would function normally, unless you "knew how to ask". I remember in one chase scene, the protagonist could not get away until he held his hand over something that looked like a glass disk embedded in the gas can, and asked, "Please". Then the motorcycle transformed into a hover bike and got the protagonist out of the tight spot.
I remember the episode ended when he went to something of a below-ground alien house, ship or bunker, but I don't remember much else.
I'm not expecting much, but it's a question that's been gnawing at the back of my mind, for at least a decade or so.