There are secret bosses in the game that require completing all Liberation Missions (including Nebula Area Liberation Missions).

Boss	How to unlock
Bass/Forte SP	Defeat Chaos Lord Bass/Forte V3.
Chaos Lord - Bass/Forte V3	Defeat all 6 DS navis with an average time between 25-40 seconds.
Chaos Lord - Megaman/Rockman DS	Defeat all 6 DS navis with an average time under 25 seconds.
Chaos Lord - Nebula Gray V2	Defeat all 6 DS navis in Nebula Area6.
Chaos Lord - Nebula Gray V3	Defeat all 6 DS navis with an average time over 40 seconds.