In the land of Jhamora, the Lockni and Nohrin live in an uneasy truce fifteen years after a contentious past. It was then that King Zahn (voice of LOUIS GOSSETT, JR.) of the winged Nohrin sent out scouts to find a new place for his people to live after theirs became barren. The grounded and mystical stone worshipping Lockni accepted them with welcome arms, but the King's sister, Sedessa (voice of ANNE BANCROFT), ended up slaughtering many of them. When she then killed her own Queen, Zahn had her wings cut off and banished her forever, but the damage was already done and the Lockni haven't trusted their neighbors ever since.
Chief among them is teenager Delgo (voice of FREDDIE PRINZE, JR.) who -- despite the pacifist teachings of Elder Marley (voice of MICHAEL CLARK DUNCAN) -- doesn't like them, mainly because they killed his parents when he was just a child. Even so, when he and his best friend, Filo (voice of CHRIS KATTAN), run into Princess Kyla (voice of JENNIFER LOVE HEWITT) who's crossed over the border into their land, Delgo attempts to help her.
That doesn't sit well with General Bogardus (voice of VAL KILMER) or Colonel Raius (voice of MALCOLM McDOWELL) who come to her supposed defense and escort her back to the kingdom. But Raius isn't as loyal as he may seem, as he's actually in cahoots with Sedessa who's holed away with her gremlin-like assistant, Spig (voice of ERIC IDLE), and his hulking but dimwitted brother, Spog.
With Raius' help, Sedessa is plotting to overthrow her brother and assume control of the Nohrins, and thus the two set a plan into motion where they'll stoke the mistrust and hatred between the two races. As a result, Delgo and Kyla, despite their differences, try to foil the nefarious scheme.