Bret Stiles knows who Red John is and they are working together to take down the Tyger Tyger corporation.

There was a very popular theory I read months ago that Red John is the son of the old leader/founder of Visualize. It was the best theory I had read at that time and now I am going to expand on it because I believe it is true.

Here is a line from the poem 'The Tyger' by William Blake.
Did he who made the Lamb make thee?
Did he who made Visualize, make Red John?

I also believe the Tygers framed Bret Stiles for the death of Red John's father (The old leader of Visualize) and Bret Stiles is innocent. Red John knows this so is on a hunt to take down the Tygers.