Jane did put explosives in his house... Did you see Rigsby's map of people when the second bomb exploded? Did you see the way Jane looks at the RJ smiley face and walks across his house with an air of finality? And I think Jane had recently come off a case where he helped a drone company, so he could have called in a favour for military-grade bombs.
At the start of that episode, Red John sends a note to Bret Stiles saying "He's looking for you," the 'n's are notably the same as the murder note at Sophie Miller's house. Bret Stiles had been missing since the list of suspects tape was released. I don't think there's a coincidence. Red John asked Bret Stiles to disappear, using the FBI cold case as an excuse.
When Jane gets the information about the 'three-dots,' he says he has *leverage*. That is not a word to say you've got a defining clue. It means, he knew the three-dots would not be enough to find Red John. Jane was after something else. Jane finally had an excuse to draw out Stiles.
If Red John was Brett Partridge, Stiles' knowledge is the best chance for Jane to find Partridge. But Stiles wasn't going to just give up his whereabouts. Stiles said, "I shall return!"
Then there's a missing episode, where Jane should have captured and killed Partridge and we got the answers to the mystery. But in place of this episode, was a silly episode, which bordered on playful at times, but mainly silly.
Then, 2 years later, some guy called Roger is at the beach... he speaks English. "He's not a great talker," Jane said. Stiles said he'd return... was this his return? He looks a broken man. Did Jane break him? Did Stiles give up Red John? Since season 6 resumed, we find out Red John is dead. But Red John may not have been McAllister, as we hear that Jane never specifically admitted to killing McAllister by the testimony at Jane's fake trial. And Jane also says at one point, he's killed the man who killed his wife and kids. There's a lot of tip-toeing around the exactitude of the situtation.
In conclusion, episode 8 just doesn't fit with the story before or the story after and could easily be re-done. An alternate ending wouldn't actually hurt in this instance as it would be easy to fit in a Partridge ending, because it would fit in so seamlessly.
