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Prior to the events of the season 3 finale of Fringe, the Broyles from Over There (i.e. Col. Broyles) died. After the events of that finale, a character was wiped from history. Col. Broyles was killed and used as the mass sent Over Here to replace the Olivia from Over There (i.e. Fauxlivia) when they brought her back Over There.

It seemed like his death was a key part of the events of the escalating conflict between the two Earths. But in S4E2, One Night in October, we see Col. Broyles alive and well. We also know Fauxlivia still went on her mission Over Here, thanks to Walter saying as much. So is Col. Broyles still alive, and if so how? We know that the now-missing character's disappearance altered the history we've seen over the past 3 seasons, how did the events around Broyles' death change in this new history?

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    I have a sneaking suspicion that we are now watching events unfold in a third universe. That explains Nina, among other things.
    – Adele- Nexus of Potlucks
    Commented Dec 12, 2011 at 20:42

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It's because he did not die in the alternate time line created at the end of the season 3.

He is not alone, in "Subject 9" (episode 4 of season 4), they find Cameron James, a subject of Cortexiphan trials:

Cameron and Olivia talk about the other test subjects from Jacksonville. Has she heard about any of the others? Olivia has not. He is the only other test subject she knows anything about. The same goes for him - no contact with the others.

But, in Over There, Part 1 (the first part of the season 2 finale), Olivia needed the help of 3 others Cortexiphan test subjects (James Heath, Sally Clark and Nick Lane) to switch universes. Since she never met them in the alternated time line, they did not die and Olivia never switched universe by these means. Others clues in the early season 4 indicate that she has not mastered her abilities (yet).

When Col. Broyles died in the season 3 episode Entrada, his body was used as a counterweight for Fauxlivia's recuperation, but the Olivia from Over Here returned by her own means. This cannot be the way she returned in the new alternate timeline, since everything indicates she never switched universes by herself since she quit the Cortexiphan trials.

She probably returned to Over Here as Fauxlivia's counterweight, as it was originally planned. Anyway, this make the treason of Col. Broyles unnecessary, as it was to help Olivia to reach the isolation tank in the Harvard lab so she could concentrate and switch universes.

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In S4E2, Walter mentioned that Olivia was kidnapped to the other side, not Peter being kidnapped and her following. I think that with that significant change, she probably did not interact with Broyles. Walternate would have kept her captive and experimented on her instead of trying to brainwash her into believing she was Fauxlivia.

Also, I don't think this is something the writers planned too far in advance. I looked back to S3E22, the final episode of season 3, at the very end, when the two worlds come together. We see both Olivia's and both Walters, but we only see the Broyles from 'our' side. If the writers had been planning this back then, I think the other Broyles would have 'magically' appeared at that time.

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Maybe, just maybe, Walternate replaced Broyles on his side with a shape shifter because I seem to recall his team thought he just disappeared

As I watch the episode, SE4 The Consultant, the idea of shape shifters is viable ONLY if they take on the emotions of the 'bodies' they inhabit. Remember, in last week's episode, the shape shifter who took on (and killed) multiple victims, STILL carried the picture of his 'real' son. Nothing suggested he had any emotional attachment to the loves ones of the victims he inhabited.

With that in mind, it is not consistant for Col. Broyles body to have been occupied by a shape shifter because Col. Broyles is acting as a mole to save his son. A shape shifter would have no love for that child.

For these reasons, the reappearance of Col. Broyles, 'back from the dead,' remains unexplained.

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Go to http://tvovermind.zap2it.com/fox/fringe/review-fringe-season-4-puts-strange-world/92224 There is an article that states the existance of Broyles might be due to Peter not existing - the timeline may have changed, also the writers may have an explanation in an episode to come - either way people have noticed so there will have to be a good reason for his "resurrection".

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  • I've edited the question to make it clearer that I know Peter's disappearance caused this, I'm looking for details on how the history we saw play out in S3 has changed in this new timeline. What happened instead of Broyles dying? Did he not assist Olivia, so he wasn't punished with death?
    – user1027
    Commented Oct 1, 2011 at 3:17
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This really bothers me because either way, Fauxlivia would have had to be replaced mass wise with something from the other side. There's no way Olivia could have escaped without col. Broyles help, so the events don't seem to have changed even with / without the missing character.

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How about this: what if Fauxlivia stayed Over Here until the bridge was created, thereby not needed an exit and not using Broyles as a mass-replacement? This plot hole is really bothering me.

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Well since Olivia was kidnapped I'm assuming they sent Olivia back at the same time as brining fauxlivia back which means they didn't have to replace her mass with the other broyles which means the other broyles didn't help her escape and never did anything wrong to be killed

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We know that 'Over There' they are far more advanced technologically and medically. In the first episode of season 4 we see Walter reanimate a dead bird which briefly flies around the lab. Perhaps they sent Colonel Broyles back soon enough so they were able to save him?

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