Made a few big typo's. Repost. Sorry to be irksome.
Here is what I think happened: Gale Bertram, McAllister, and Smith all work for Tyger Tyger.
Gale Bertram, McAllister and Smith ALSO work for Robert Kirkland. Robert planted spies in Tyger Tyger so he could uncover the conspiracy. Who convinces Minelli to retire? It can be seen in season 2, its Kirkland! Then Bertram arrives later :) In the episode, Gale Bertram leaves a flash drive, full of names of everyone in Tyger Tyger in the safe.
Red John thinks Bertram is playing a loyal footsoldier in pretending that he's Red John. However Bertram is complying with Patrick's plan. Patrick has been sedated. He's completely unharmed from the blast. Gale Bertram is completely unharmed. Bertram is the one who sedated Patrick before the blast. Reede Smith is completely unharmed then takes a freaking bullet for Patrick's plan- he's a stand up hero. Patrick doesn't need to tell Bertram to go and play his role well. Bertram is a stand up guy, acting for the greater good.
However this is what we think happened in the house.
Ray Haffner is told to lift up his shirt properly, revealing a vertical tattoo. Patrick fires a gunshot pointing above him. The bullet makes Haffner scream, even though it missed. Lisbon's phone is bugged by Red John. He hear's Haffner plead and the bullet. Later he hears Patrick blew everyone up. Remember who Patrick helped in episode 2? A weapon designing company. Its about time Patrick gets a reward for doing all those cases.
There's a long pause between the bomb and the bullet. Patrick issues orders to McAllister. McAllister kidnaps Bret Stiles and Ray Haffner. You can see him leaving the scene in another larger car.
Bertram and Reede Smith are ordered by Patrick to become fugitives after they're seen by Lisbon. These are loyal men. They are acting for the greater good. They will do anything to uncover the Tyger Tyger conspiracy, they will give their own lives, or even take others.
At the end of the episode Patrick is done. He has won by destroying Tyger Tyger. Bertram has given CBI the list of names. McAllister has taken Stiles and Ray Haffner- The Visualize links. HOWEVER by making Red John think he's won, Patrick lures Red John like he did in season 4. When Patrick says to Lisbon "I'm letting go," Red John hears because she's bugged. Red John sends a man on his behalf to say to Patrick "I've won". Patrick shoots him once, but Patrick has known, since Lorelei Martins told him he's met Red John, that Red John is Brett Partridge (Harker's description.) The man in the cathedral is not Red John, but Patrick pretends he is. He shoots him once then shows him mercy.
After that the real Red John is confident Patrick will not kill him, so he agrees to meet Patrick. And I really hope Patrick's blue teacup was not smashed in vain.
Patrick is then wanted by the FBI for charges of fraud after everyone discovers what he really did, so Patrick flees to Mexico.
