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Clear the game with certain normal characters will unlock other secret characters in the game.
(Once you unlock them, you have to fight in VS Mode and these characters will join in the battle. You then need to defeat them)
Alternative Way - Gogandantess
Clear the game with all 12 normal characters in story mode to unlock him.
Gogandantess
Have Samanosuke Akechi, Kaede, Normal Soldier and Kotarou each fight against Gogandantess to unlock him.
Jujudormah
Ran Clear the game with Jujudormah twice in story mode.
Kojirou Sasaki
Clear the game with Miyamoto Musashi in Story Mode
Miyamoto Musashi
Clear the game with Small Fish Soldier in Story Mode
Nobunaga Oda
Clear the game with all 12 normal characters in story mode to unlock this warlord.
Rockman EXE
Clear the game with Samanosuke Akechi in story mode.
Zero
Use Rockman EXE to collect all 3 Crystals (Green, Blue, Purple) to unlock Zero
Zero Parts
Blue Z-part: Complete Phantom Realm 2 with Megaman EXE.
Green Z-part: Complete Phantom Realm with Megaman EXE.
Red Z-part: Complete Story mode with Megaman EXE.
More Victory Souls
When you are playing in the Phantom Realm, let the souls be sucked up by the Gyaran (the floating ball of skulls). After you let this happen to a couple victory souls, destroy the Gyaran and all the souls that were sucked up by the Gyran will now be doubled