There is a definite fire in the Mankey's eyes from his life in the wild, but the look you see is undoubtedly one of gratitude and admiration. Both he and you had seen the Pikachu ruthlessly put down every other Mankey he had been traveling with, and you had the guts and compassion to stand between him and it.
The Mankey lost all of his friends. You protected it when no one else could. It's ready to return the favor to you whenever. He looks at the pokeball, looks at you, and nods.