Showing how he can’t take responsibility for what he did to Anya. However, at the end of the level no matter what you do the baby/creature catches up to him showing how he can’t run away from this.

Because the creature is an amalgamation of the company's mascot I think the creature is also meant to represent how he was the one to crash the ship and get them into this situation. So by him running away from it, he’s trying to avoid all responsibility.