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***** The Cortexiphan trials most certainly did not take place for over six years. Originally, Olivia was supposed to be 3 when the experiments took place. The vision she had during the Season 2 episode when she was injected with Cortexiphan again had her 3-year old self in it. It correlates with her not remembering any of it. I find it very hard to believe a 9-year old Olivia would forget being injected with drugs or traveling to another universe, unless Walter somehow removed her memories. I see this as a clumsy retcon tying Peter and Olivia together in their childhoods. Don't get me wrong, it's a great episode, but continuity-wise, it doesn't mesh with what we knew before.



** No. The physicist is bodily transplanted in time.



*** None of this are as yet plot holes. They may turn out to have perfectly reasonable explanations.



** While I agree Peter's presence being a paradox doesn't make much sense given what we know, I think the reason the Observe can't go back in time to warn his past-self, because he does not have a past self. As "The Firefly" showed, the Observers can move through time without any repercussions. Walter postulates that they exist outside of time, simultaneously at all points in it. Hence, he is one self and cannot interact with his past self. Just an idea.



** Perhaps they use the devices to "renew" themselves without actually changing form?

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** Perhaps they use the devices to "renew" themselves without actually changing form?form?
* Here's something that bugs me - John Scott. The handwave that John was a Black Ops NSA agent and that's why he knew so much about the Pattern felt like so much bull. Why, then, did he kill that guy (name escapes me - the villain of the pilot, the guy with the twin brother) after recovering? To keep his cover? Why did he threaten the guy at the beginning of the episode? Was he in on the testing of the toxin on the plane? If so, then I honestly don't think being undercover justifies knowing about an experiment that will kill 147 people in a most horrific manner and keeping quiet about it. What, he couldn't slip a note to his handler?
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* Going back to Season 2, there is an inconsistency with how Walternate's shapeshifters work. The shifter who killed Charlie was starting to fall apart after he lost his device and couldn't change into a new form. The other shifter tells him that he'll die if he doesn't get a replacement. But when Newton contacts the "sleeper" agents, it's clear that several of them have held the same form for years at a time. So how long can a shifter hold a single identity?

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* Going back to Season 2, there is an inconsistency with how Walternate's shapeshifters work. The shifter who killed Charlie was starting to fall apart after he lost his device and couldn't change into a new form. The other shifter tells him that he'll die if he doesn't get a replacement. But when Newton contacts the "sleeper" agents, it's clear that several of them have held the same form for years at a time. So how long can a shifter hold a single identity?identity?
** Perhaps they use the devices to "renew" themselves without actually changing form?
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* Why exactly is Peter's presence a paradox? It doesn't make much sense that the Observer distracting Walternate is a "mistake" and then turn around and have undoing the fix of that mistake somehow resolve the same paradox. And why didn't he just keep his past self from distracting Walternate in the first place? That would be the simplest solution to all the universe-hopping bull and would probably keep everyone happiest. (Please don't trot out the "BlueAndOrangeMorality" bullshit because that's an excuse, not a reason)

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* Why exactly is Peter's presence a paradox? It doesn't make much sense that the Observer distracting Walternate is a "mistake" and then turn around and have undoing the fix of that mistake somehow resolve the same paradox. And why didn't he just keep his past self from distracting Walternate in the first place? That would be the simplest solution to all the universe-hopping bull and would probably keep everyone happiest. (Please don't trot out the "BlueAndOrangeMorality" bullshit because that's an excuse, not a reason)reason)
* Going back to Season 2, there is an inconsistency with how Walternate's shapeshifters work. The shifter who killed Charlie was starting to fall apart after he lost his device and couldn't change into a new form. The other shifter tells him that he'll die if he doesn't get a replacement. But when Newton contacts the "sleeper" agents, it's clear that several of them have held the same form for years at a time. So how long can a shifter hold a single identity?
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* ''Novation''. Shapeshifters. They fell for it '''AGAIN.'''

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* ''Novation''. Shapeshifters. They fell for it '''AGAIN.''''''
* Why exactly is Peter's presence a paradox? It doesn't make much sense that the Observer distracting Walternate is a "mistake" and then turn around and have undoing the fix of that mistake somehow resolve the same paradox. And why didn't he just keep his past self from distracting Walternate in the first place? That would be the simplest solution to all the universe-hopping bull and would probably keep everyone happiest. (Please don't trot out the "BlueAndOrangeMorality" bullshit because that's an excuse, not a reason)
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*** Yes, there is in fact a major discrepancy. After Olivia and Bell collect Walter from the hospital, there is a scene where they decide to split up so that Walter and Bell can go build a "doorstop" to keep the crack that Olivia will create open, because they fear that without the other Cortexiphan kids, she won't be strong enough to keep it open on her own. Twenty minutes later, they're saying it the other way around, that the "doorstop" device is supposed to open the crack, and Olivia is supposed to keep it open, and by the end of the episode, the device opens the crack, and Bell's own bodily energy keeps it open. The episode is inconsistent the whole way through on this particular point. I mean, I understand that they had to get Fauxlivia over there for purposes of the story, but what's bothersome is that they seemed to have forgotten to alter the rest of the episode's dialogue once they decided they would change the ending to allow this.
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* In the episode with the killer fungus, why did nobody bother with protective suits when they went underground? They all wore hazmat suits at the morgue after the spores were released, but in a heavily infested area where two people had died already nobody thought there was any danger, even after the fungus was revealed to be sentient and willing to defend itself.

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* In the episode with the killer fungus, why did nobody bother with protective suits when they went underground? They all wore hazmat suits at the morgue after the spores were released, but in a heavily infested area where two people had died already nobody thought there was any danger, even after the fungus was revealed to be sentient and willing to defend itself.itself.
* ''Novation''. Shapeshifters. They fell for it '''AGAIN.'''
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* Wait, isn't alt!Broyles [[spoiler: ''dead''? So how is he alive in episode 2 of season 4 as if nothing happened? All that was left of him was a torso. [[FlatWhat What]]. Yeah ok, I guess they could argue because of Peter's existence being erased it changed things, but they keep referencing Olivia being kidnapped and the equivalent exchange of finally returning her is what killed alt!Broyles. Don't even get me started on the whole Peter's existence being wiped and what it doesn't, but should, change.]]

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* Wait, isn't alt!Broyles [[spoiler: ''dead''? So how is he alive in episode 2 of season 4 as if nothing happened? All that was left of him was a torso. [[FlatWhat What]]. Yeah ok, I guess they could argue because of Peter's existence being erased it changed things, but they keep referencing Olivia being kidnapped and the equivalent exchange of finally returning her is what killed alt!Broyles. Don't even get me started on the whole Peter's existence being wiped and what it doesn't, but should, change.]]]]
** Peter's erasure has changed a number of things - Walter's personality has changed, Lincoln has never met the team; the kidnapping could easily have gone differently in the new timeline. Maybe Olivia and Alt!Olivia just switched normally, or she managed to pull off the dimension hopping herself, or someone else died in Broyles' place.
* In the episode with the killer fungus, why did nobody bother with protective suits when they went underground? They all wore hazmat suits at the morgue after the spores were released, but in a heavily infested area where two people had died already nobody thought there was any danger, even after the fungus was revealed to be sentient and willing to defend itself.
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**** I saw Walter's reaction as "I didn't expect that", which doesn't necessarily mean "I didn't know she could do that".
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** Fauxlivia's just as bad. They have the justification that she had been fed information about Olivia regarding details of her life but really, when someone comes back from a trip to an alternate universe where there are not only shapeshifters, but also alternate versions of yourselves I would have thought the fact that she suddenly started acting strangely afterward should have thrown up a red flag. There's only so many times someone can play off "Oh, I would/did? Hahahaha" before you really should pick up on something.

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** Fauxlivia's just as bad. They have the justification that she had been fed information about Olivia regarding details of her life but really, when someone comes back from a trip to an alternate universe where there are not only shapeshifters, but also alternate versions of yourselves I would have thought the fact that she suddenly started acting strangely afterward should have thrown up a red flag. There's only so many times someone can play off "Oh, I would/did? Hahahaha" before you really should pick up on something.something.
* Wait, isn't alt!Broyles [[spoiler: ''dead''? So how is he alive in episode 2 of season 4 as if nothing happened? All that was left of him was a torso. [[FlatWhat What]]. Yeah ok, I guess they could argue because of Peter's existence being erased it changed things, but they keep referencing Olivia being kidnapped and the equivalent exchange of finally returning her is what killed alt!Broyles. Don't even get me started on the whole Peter's existence being wiped and what it doesn't, but should, change.]]
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** From what we saw, it can be used to forcibly close artificial portals between worlds. There is nothing to suggest that it could plug a vortex.
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* What happened to the device at the end of season one that closes holes in reality? Wouldn't that eliminate the need for amber and such?

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* What happened to the device at the end of season one that closes holes in reality? Wouldn't that eliminate the need for amber and such?such?
* Why aren't the main characters more vigilant about checking peoples' identities? Charlie's death was bad, his team knew they were dealing with a shapeshifter who can change on the fly, then (after they've split up) Charlie easily dispatches it. I feel like that could have been dealt with if anyone had gone and said "hey... what's my favorite color?"
** Fauxlivia's just as bad. They have the justification that she had been fed information about Olivia regarding details of her life but really, when someone comes back from a trip to an alternate universe where there are not only shapeshifters, but also alternate versions of yourselves I would have thought the fact that she suddenly started acting strangely afterward should have thrown up a red flag. There's only so many times someone can play off "Oh, I would/did? Hahahaha" before you really should pick up on something.
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** He did but because Nina grabbed him the vial with the medicine shattered so he had to improvise.

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** He did but because Nina grabbed him the vial with the medicine shattered so he had to improvise.improvise.
* What happened to the device at the end of season one that closes holes in reality? Wouldn't that eliminate the need for amber and such?
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* Why didn't Walter just bring the medicine with him when he crossed over to the other universe, so as to cure Peter then and there?

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* Why didn't Walter just bring the medicine with him when he crossed over to the other universe, so as to cure Peter then and there?there?
** He did but because Nina grabbed him the vial with the medicine shattered so he had to improvise.
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** This isn't so much a plot hole as something made intentionally vague as part of the season finale cliffhanger. The mystery of what the hell just happened there is presumably going to play a major part in season four, or at least the first few episodes of it.
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** 4-What is Walternate's connection to Sam? And why can't he trust him?

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** 4-What is Walternate's connection to Sam? And why can't he trust him?him?
* Why didn't Walter just bring the medicine with him when he crossed over to the other universe, so as to cure Peter then and there?
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** 2-For all intensive purposes, he's revealed to just have been an ordinary guy with knowledge passed down his family. That said, how did he exactly know about the other Olivia, Peter and his connection to the machine, and why did he tell Nina that Peter must choose one Olivia or the other when that clearly wasn't the case, and he knew it.

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** 2-For all intensive intents and purposes, he's revealed to just have been an ordinary guy with knowledge passed down his family. That said, how did he exactly know about the other Olivia, Peter and his connection to the machine, and why did he tell Nina that Peter must choose one Olivia or the other when that clearly wasn't the case, and he knew it.
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** 3-The First People are, technically, Walter and co. from the future - the "technology of the first people" was nothing more than a sort of time machine, along with other goodies, sent by Walter back in time through a wormhole. If the technology was developed by him, then why does it appear so alien in nature? Why does Walter comment that the Wave Sink Device looks an awful lot like a William Bell Design? The "instructions" dug up by the Weiss family also reveals a completely alien language accompanied by pieces of the machine. And lastly, what exactly is the deal with, and ultimately purpose, with those creepy number stations that first revealed the existence of the "First People"?

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** 3-The First People are, technically, Walter and co. from the future - the "technology of the first people" was nothing more than a sort of time machine, along with other goodies, sent by Walter back in time through a wormhole. If the technology was developed by him, then why does it appear so alien in nature? Why does Walter comment that the Wave Sink Device looks an awful lot like a William Bell Design? The "instructions" dug up by the Weiss family also reveals a completely alien language accompanied by pieces of the machine. And lastly, what exactly is the deal with, and ultimately purpose, with those creepy number stations that first revealed the existence of the "First People"?People"?
** 4-What is Walternate's connection to Sam? And why can't he trust him?
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* I know he's supposed to be an OmnidisciplinaryScientist, but seriously. [[OnceAnEpisode Every single anomaly]] they investigate is invariably liked to Walter's work for the military/government/whatever. I know it [[NecessaryWeasel has to be that way for the show to function]], but it would have been nice to have one or two episodes where there's a Pattern event and for Walter to say, "sorry, no idea, never worked on anything like ''that''".

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* I know he's supposed to be an OmnidisciplinaryScientist, but seriously. [[OnceAnEpisode Every single anomaly]] they investigate is invariably liked to Walter's work for the military/government/whatever. I know it [[NecessaryWeasel has to be that way for the show to function]], but it would have been nice to have one or two episodes where there's a Pattern event and for Walter to say, "sorry, no idea, never worked on anything like ''that''".''that''".
* There are...quite a few plot holes when Sam Weiss and the First People are concerned. Might as well list them all...:
** 1-How did Sam get his hands on Walter's "universal window"? On top of the other weird toys he's seen with.
** 2-For all intensive purposes, he's revealed to just have been an ordinary guy with knowledge passed down his family. That said, how did he exactly know about the other Olivia, Peter and his connection to the machine, and why did he tell Nina that Peter must choose one Olivia or the other when that clearly wasn't the case, and he knew it.
** 3-The First People are, technically, Walter and co. from the future - the "technology of the first people" was nothing more than a sort of time machine, along with other goodies, sent by Walter back in time through a wormhole. If the technology was developed by him, then why does it appear so alien in nature? Why does Walter comment that the Wave Sink Device looks an awful lot like a William Bell Design? The "instructions" dug up by the Weiss family also reveals a completely alien language accompanied by pieces of the machine. And lastly, what exactly is the deal with, and ultimately purpose, with those creepy number stations that first revealed the existence of the "First People"?
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** This is thoroughly and completely explained in the episode! Just watch it and you'll see there IS no discrepency here.

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*** That would be logical, were it not for the fact that when the 3YO Olivia starts the fire the response from Walter and Bell is shock that she does it. If that was so, why would they experience similar shock when it happens again in Subject 13? They'd already know what she was capable of. Yet they don't appear to be.

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*** That would be logical, were it not for the fact that when the 3YO Olivia starts the fire the response from Walter and Bell is shock that she does it. If that was so, why would they experience similar shock when it happens again in Subject 13? They'd already know what she was capable of. Yet they don't appear to be. They act as though they've never seen her do that before.


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** Yes, it's one of the documented differences between our universe and theirs - they spell it differently.

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** In Subject 13, we saw her start ''a'' fire, not necessarily ''the'' fire. Given all the other discrepancies, this troper is confident they were two different events.

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** In Subject 13, we saw her start ''a'' fire, not necessarily ''the'' fire. Given all the other discrepancies, this troper is confident they were two different events. events.
*** That would be logical, were it not for the fact that when the 3YO Olivia starts the fire the response from Walter and Bell is shock that she does it. If that was so, why would they experience similar shock when it happens again in Subject 13? They'd already know what she was capable of. Yet they don't appear to be.
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**In Subject 13, we saw her start ''a'' fire, not necessarily ''the'' fire. Given all the other discrepancies, this troper is confident they were two different events.
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*** As it stands now, he seems to have [[spoiler: "fulfilled his purpose," whatever the heck that means, but it implies that he wiped himself from the timestream by some sort of paradox]], but that just raises ''more'' questions.
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** So, did the Observers [[spoiler: delete Peter, or did he do himself in by mucking with the timestream somehow?]]

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** So, did the Observers [[spoiler: delete Peter, or did he do himself in by mucking with the timestream somehow?]]somehow?]]
* I know he's supposed to be an OmnidisciplinaryScientist, but seriously. [[OnceAnEpisode Every single anomaly]] they investigate is invariably liked to Walter's work for the military/government/whatever. I know it [[NecessaryWeasel has to be that way for the show to function]], but it would have been nice to have one or two episodes where there's a Pattern event and for Walter to say, "sorry, no idea, never worked on anything like ''that''".
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** Also, what does this mean for [[spoiler:Fauxlivia's baby? Does he still exist?]]

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** Also, what does this mean for [[spoiler:Fauxlivia's baby? Does he still exist?]]exist?]]
** So, did the Observers [[spoiler: delete Peter, or did he do himself in by mucking with the timestream somehow?]]
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** Also, what does this mean for [[Fauxlivia's baby? Does he still exist?]]

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** Also, what does this mean for [[Fauxlivia's [[spoiler:Fauxlivia's baby? Does he still exist?]]
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* Hold on while I try to walk myself through this. Spoilers for very recent events, this being about the ending of episode 3x22. So, after the events at the end, it seems that [[spoiler: no one has any memories of Peter once he vanishes after leaving the machine and making the bridge between worlds.]] The observers imply [[spoiler: that he never existed//was wiped from the time stream because he has now served his purpose.]] Um, what? [[spoiler: If Peter is the focal point for basically everything that goes on or has gone on in the series all because our Walter's Peter died as a child, which caused him to go to the other side and steal their Peter which caused the universe to start breaking down which caused basically everything else, then wouldn't it follow that if you [[CosmicRetcon retcon]] Peter out of existence, don't you undo everything? Doesn't it then follow that by taking him out of things you make it so that none of this ever happened?
** Also, what does it mean for Fauxlivia's baby? Does he still exist?]] I am so freaking confused right now.

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* Hold on while I try to walk myself through this. Spoilers for very recent events, this being about the ending of episode 3x22. So, after the events at the end, it seems that [[spoiler: no one has any memories of Peter once he vanishes after leaving the machine and making the bridge between worlds.]] The observers imply [[spoiler: that he never existed//was wiped from the time stream because he has now served his purpose.]] Um, what? [[spoiler: If Peter is the focal point for basically everything that goes on or has gone on in the series all because our Walter's Peter died as a child, which caused him to go to the other side and steal their Peter which caused the universe to start breaking down which caused basically everything else, then wouldn't it follow that if you [[CosmicRetcon retcon]] Peter out of existence, don't you undo everything? Doesn't it then follow that by taking him out of things you make it so that none of this ever happened?
** Also, what does it mean for Fauxlivia's baby? Does he still exist?]]
happened?]] I am so freaking confused right now.now.
** Also, what does this mean for [[Fauxlivia's baby? Does he still exist?]]

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* Hold on while I try to walk myself through this. Spoilers for very recent events, this being about the ending of episode 3x22. So, after the events at the end, it seems that [[spoiler: no one has any memories of Peter once he vanishes after leaving the machine and making the bridge between worlds.]] The observers imply [[spoiler: that he never existed//was wiped from the time stream because he has now served his purpose.]] Um, what? [[spoiler: If Peter is the focal point for basically everything that goes on or has gone on in the series all because our Walter's Peter died as a child, which caused him to go to the other side and steal their Peter which caused the universe to start breaking down which caused basically everything else, then wouldn't it follow that if you [[CosmicRetcon retcon]] Peter out of existence, don't you undo everything? Doesn't it then follow that by taking him out of things you make it so that none of this ever happened?]] I am so freaking confused right now.

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* Hold on while I try to walk myself through this. Spoilers for very recent events, this being about the ending of episode 3x22. So, after the events at the end, it seems that [[spoiler: no one has any memories of Peter once he vanishes after leaving the machine and making the bridge between worlds.]] The observers imply [[spoiler: that he never existed//was wiped from the time stream because he has now served his purpose.]] Um, what? [[spoiler: If Peter is the focal point for basically everything that goes on or has gone on in the series all because our Walter's Peter died as a child, which caused him to go to the other side and steal their Peter which caused the universe to start breaking down which caused basically everything else, then wouldn't it follow that if you [[CosmicRetcon retcon]] Peter out of existence, don't you undo everything? Doesn't it then follow that by taking him out of things you make it so that none of this ever happened?]] happened?
** Also, what does it mean for Fauxlivia's baby? Does he still exist?]]
I am so freaking confused right now.
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** Olivia actually apologizes to him for this in ''"Reciprocity"''... and I don't recall anyone calling Peter out other than her.

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** Olivia actually apologizes to him for this in ''"Reciprocity"''... and I don't recall anyone calling Peter out other than her.her.
* Hold on while I try to walk myself through this. Spoilers for very recent events, this being about the ending of episode 3x22. So, after the events at the end, it seems that [[spoiler: no one has any memories of Peter once he vanishes after leaving the machine and making the bridge between worlds.]] The observers imply [[spoiler: that he never existed//was wiped from the time stream because he has now served his purpose.]] Um, what? [[spoiler: If Peter is the focal point for basically everything that goes on or has gone on in the series all because our Walter's Peter died as a child, which caused him to go to the other side and steal their Peter which caused the universe to start breaking down which caused basically everything else, then wouldn't it follow that if you [[CosmicRetcon retcon]] Peter out of existence, don't you undo everything? Doesn't it then follow that by taking him out of things you make it so that none of this ever happened?]] I am so freaking confused right now.
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** Sam Weiss was using it in a recent episode so its not like the writers forgot it. Which makes it even more puzzling. I'm going to say that the knowledge to create the device was lost when Bell performed that surgery on Bishop. The existing window could then have been destroyed or taken by Weiss in the years between.

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