The game ended with the seaplane out of commission and the Master fleeing back into the jungle.
The result of the 2 games was the Master was still out in the jungle with a booby-trapped briefcase containing Formula X. The Master survived to gain a couple skills, while Agent 9 gained more men (supporters).
Aaron (The Master) and Sam (Professor White and Ninja Sam) are brothers, and like all good brothers, when gaming, concetrate on attaking each other first.