Albus mode is an alternate continuity in which Albus went on his mission as he was supposed to.Albus travels around, fighting all of the enemies that Shanoa would have fought had Albus discovered Barlowe's plans, while Shanoa is busy spending those weeks regaining enough of the skill she lost when her memories were sacrificed to Dracula to use Dominus on the seal. When you encounter "yourself", it's not you, but a doppelganger. In the pre-battle dialogue that we don't see, it's revealed that the doppelganger was sent by Barlowe when he discovered Albus's mission was almost complete in order to keep him from coming back too soon and interrupting the ceremony. It is at this point, in seeing how Barlowe can summon such high-level dark creatures to do his bidding, that Albus discovers Barlowe's treachery, and that Shanoa is about to die. When you kill the doppelganger, it isn't the doppelganger that's yelling Shanoa's name, it's the real Albus, now racing back to Ecclesia to try and save Shanoa... only to be too late. Needless to say, when he gets back and Shanoa's nowhere to be found, he kills Barlowe out of rage, steals Barlowe's notes, and discovers that by modifying his "glyph in bullet" technique he can imbue his gun with the ability to harm Dracula, and proceeds to go off to stop Dracula once and for all, having nothing left to fight for.