You, your friend, and Octavius have joined together as a temporary team. It sounds crazy, but there was an explanation for it. Your friend needed answers, and Octavius needed his invention, which Hydra took over along with Otto's other research. You went with them to make sure your friend was okay.
In the midst of a battle with the creatures on the ship, Otto escaped. At least that's what you thought, still not trusting the scientist, but he returned a few minutes later in a new guise. His limbs were no longer atrophied, his black hair became short and brown, and the huge tentacled mechanisms were replaced by a more comfortable and dangerous version. Well, Otto was actually a man of his word, because he didn't run away and was going to fulfill his end of the bargain, proud of his new body.