Mark Rubbed Some People the Wrong Way

There are two problems with this theory. Most Mark was known for his no drug policy on the ship, which is the reason why he fired John. If some sort of drug cartel had made it to Craig Alaska to kill Mark, that would have stuck out like a sore thumb. In a town filled with fishermen, outsiders would have been pretty easily spotted. But in a busy port like Craig, you would figure someone like this would have been seen.