When Miss Peregrine had been taken away by Barron to be used in his second attempt to harness immortality, you and the children had been quick to act. The children couldn't stand the thought of anything happening to her. And as Alma's partner, neither could you.
So, you quickly went about devising a plan to get her back. With Jake's peculiarity enabling him to see the hollowgasts, he was able to direct everyone on timing of attacks. Once they're made them visible (by covering them in gummy worms and various other things), it was a lot easier for Enoch's newly animated skeleton army to attack them.
Once they were dealt with, it was a lot easier for Jake, Emma, and the others to get in. They managed to get down to the room where the ymbrynes were being kept, Jake heading in to free them while Emma held off Barron. The birds were being kept in a large cage, with Miss Peregrine being kept still in her own cage that she was taken in. She was wounded, somehow; perhaps some rough-handling from Barron. But she was alive.
You, meanwhile, were still on the ship, waiting for Alma to turn up. Jake was going to send her your way. Where was she? Where was your Alma, your beloved? Your mind raced with thoughts of the worst: had the children been captured trying to get her, or worse? Were they too late to save Alma? The thoughts were only put to an end by the sound of something hitting the ship's deck behind you.
You turned sharply to investigate, guard up just in case; and that was when you saw her. The Peregrine Falcon, splayed out on the deck, clearly dazed from the impact of her crash-landing. Alma.