If you decide to go against Phineas and turn him as a prisoner of the Board. To get this ending, You have to talk to Udom Bedford when you first get to the Groundbreaker. This is where you can turn Phineas in when you talk to him. This ending is the bad ending of the game.
This will trigger your loyalty with The Board as you will start working for them instead. This will totally change the gameplay experience as you will be fighting other enemies instead of the Board soldiers. The only catch is that the prisoners that were freed by Phineas will set up a riot that gets Chairman Rockwell killed.
There is also another path in this ending where instead of turning Phineas in, you can make him take his own life. This can make things easier to achieve this ending as it will prevent you from fighting the giant robot at the end.