Theory: Nothing is controlling Brian. He acts as Hoody to remain anonymous, while trying to help out Tim and Jay.
Time was running out for Brian. Resources were becoming limited, and the Operator was closing in on him. He had to be quick, and be on his toes.
Brian felt his thoughts blur together and vision tunnel slightly as he approached the old building. Things only got worse upon entry. A few steps in he dropped the camera and fell to the ground, coughing and hacking. He tore off his mask, gasping for air, his mind still a blurry mess of disconnected thoughts. His vision had mostly blacked out and his ears were ringing, and all Brian could do was continue to cough.
Finally the coughing fit passed and Brian's senses slowly faded to normal. He pulled the mask back over his face and retrieved the camera, continuing to walk through the old building. That kind of thing had been happening to him more and more lately, and he knew it was a warning from the Operator that he was not far behind.
The one thing that had kept Brian alive and (relatively) well this whole time was the mask. He saw the connection between Alex's behavior and disappearance and the tall, faceless man, and then the other actors in Marble Hornets started disappearing, and he knew something had to be done. The hooded man with the black mask was simply a façade, a disguise so he couldn't be pinned down. He hoped that if the Operator didn't know who he was he wouldn't hurt him, and for a while, it worked pretty well. Lately, though... Brian knew his disguise wasn't going to last him much longer. He tried to help Tim and Jay as much as he could too. They had teamed up and, in Brian's opinion, were the best chance at stopping the Operator. He did what he could to buy them time.
Brian reached his hand into a pile of wood planks, pulling out a pill bottle he kept hidden there. He'd started snatching and swallowing pills ever since the time he coughed up a considerable amount of blood. It was a precaution. There was one pill left, rattling in the bottom of the bottle. He'd have to get more later. He lifted the lower half of his mask up and swallowed the pill dry, he'd have to stock up on water while he was out too.
Brian sighed a little and pulled the mask back over his face. He silently asked the universe, whatever god above was listening, to take care of Tim and Jay, and to get them all out of this mess.