Battalion Wars has a number of Unique Enemies; mostly in the sequel:
- In the first game the Xylvanian Heavy Recon (they lack a Light Recon) only appeared in the mission "Herman's Heroes". In the sequel, their Recon only appears on "Crack Squad", a co-op remake of the aforementioned level. Their Frigates and Submarines only appear as AI enemies in "Operation Nautilus", their Artillery in "Scorched Earth", and their Anti-Air Vehicles in "Ice Station X". The Xylvanian Stratodestroyer also only appears in the final mission, which is also the only appearance of the Stratodestroyer in the game.
- In the first game, the Tundran fighter only appears once as an enemy in "Behind Enemy Lines", where it appears during a setpiece being chased by Frontier Fighters. The same mission also features the Spy, a single renamed Grunt that can only be fought and killed in this mission. In the second game, the Tundran Recon's only appearance is in "Enemies Undone", their Heavy Tank and Frigate only appear as enemies "Wings of the Gunship", and their Light Tank does the same in "Line in the Sand".
- The Solar Empire Submarine only appears in "Up Periscope", the Recon and their only Dreadnought are faced in "Operation Reprimand", and the Fighter in "Their Finest Hour".
- The Spy Baloon only appears in the first level of the first game. They reappear in the second game repurposed as the Barrage Baloon, where once again they are only faced as an obstacle by the Western Frontier player in the assault map "Aces High".
- A lonely Anglo Isles Anti-Air Veteran is faced as an enemy in the co-op mission "Storm the Beaches". The Anglo Assault Veteran and Battleship also make their only appearance as a computer-controlled enemy in the same mission.
- As the least used faction, most Iron Legion units are not faced as AI enemies outside of the Prologue. The Bomber is their only unit that cannot be fought even in PvP multiplayer, despite having an antagonistic presence in a cutscene during the Prologue.
- Several missions in the second game feature turret emplacements that are exclusive to a single level. "Operation Reprimand" features a pair of RPG Towers styled as tank turrets mounted on castle walls that defend the first primary objective. "Incursion" is the only appearance of the Stolen Turret. "Crack Squad" features a unique MG Tower defending the helipad that is aesthetically styled to fit the Japanese castle wall it is adjacent to, and the skirmish map "Exchange of Fire" features a pair of AI-controlled Naval Guns that serve as a bonus objective for players to destroy.
