That massive brown Flood thing was a Compound Intelligence. It was hardwired to the Covenant ship, ready to control it when it was repaired. It's the early stage of a Gravemind. He wasn't given the normal treatment due to his importance as Captain. He represents the commanding officer of the human forces on Halo and offer the Flood invaluable tactical information and human technological system operations, along with the locations of new places to infect. Planets, space stations, ships, etc. Of course, he wasn't the only one added. Just the most recent.