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, who now desperately races 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 the lord of the night once and for all, having nothing left to fight for.
- A minor point that may support this theory is what is seen in the Game Over screen unique to Albus Mode: a fading silhouette of a distinctly female figure accompanied by bloodstains. Given that Albus primarily does everything for the sake of Shanoa in the actual canon, it would make sense that in this alternate continuity, the silhouette would be that of her. Given the details of what goes on in this alternate continuity, who's to say that the contents of that Game Over screen in-universe would not be a recurring nightmare that would haunt Albus for the rest of his days?
After beating Dracula, Shanoa left and considering that Ecclesia still existed (since it's impossible for them to be a 3-men group with just Barlowe, Shanoa and Albus) and most of them are probably also following Barlowe and his madness, Shanoa decided to dismantle Ecclesia on her own as her final mission. The Order will not stand idly and thus Shanoa has to finish off the ones she called friends before, but if she finds someone who'd listen to reason, she will let them join her. (The Castlevania Wikia implies that Shanoa destroyed the order on her own as a vengeance of how she was tricked)
In the end, Shanoa succeeded at that, and eventually swore an oath of celibacy and then became a nun (in a Shout-Out to her outfit at Castlevania: Judgment) and then lived the rest of her life near Wygol village, watching over the villagers as they resumed their training to master the Vampire Killer whip and never bearing any descendants. She also specifically told the villagers to never tell stories about her adventures so she will stay in obscurity and the effect of Ecclesia will never spread again.
