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NominSim makes an excellent case that Barty Crouch Jr. was already dying while in prison at Azkaban in his answer to this question.

“The Dementors are blind. They sensed one healthy, one dying person entering Azkaban. They sensed one healthy, one dying person leaving it. My father smuggled me out, disguised as my mother, in case any prisoners were watching through their doors. ‘My mother died a short while afterwards in Azkaban. She was careful to drink Polyjuice Potion until the end. She was buried under my name, and bearing my appearance. Everyone believed her to be me.”

Harry Potter and the Goblet of Fire, Chapter 35 (Veritaserum)

Seems that some terminal illness was slowly killing him over 11 years. (11 years is the amount of time he was free after escaping from Azkaban.) Or maybe he only had months to live and then recovered since a prisoner would be denied medical care, while somebody outside a prison could get such medical care. (e.g. - If a lifelong prisoner and a law abiding citizen both need a lung transplant to live and there is only one donor lung available, which one deserves the lung?)

What malady, if any, was slowly killing him?

RichS
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    I always assumed that it was the fact that he had been in Azkaban for around 14 years by that time, which with the constant dementor presence there, would suck the life out of anyone anyway (which is the point after all). – BMWurm Apr 21 '18 at 07:36
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    @BMWurm Barty Crouch Jr. was in Azkaban for only 2 or 3 years. He hid for 11 years after leaving Azkaban. See this answer for explanation. https://scifi.stackexchange.com/a/22952/63201 I edited my question to point out that we survived for 11 years after prison. – RichS Apr 21 '18 at 07:41
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    Right, I remembered after your edit. But maybe it was still long enough to weaken him to a point of appearing as ill as his heartbroken mother. Anyway, I'm curious for the answer, if it exists. – BMWurm Apr 21 '18 at 07:47
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    I assumed this was referring to the depression caused by a prolonged stay in Azkaban. In the same passage: “The house-elf nursed me back to health […] When I had recovered my strength, I thought only of finding my master”. – alexwlchan Apr 21 '18 at 09:14
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    Bit of a stab in the dark but do we know if My father smuggled me out, disguised as my mother is due to use of Polyjuice potion (there was obviously some in use by his mother) and since you effectively take the form of another individual perhaps you inherently get any diseases/illness as part of the package (same as losing an eye or inheriting a limp etc...) that just vanishes after the potion wears off. – Jon Clements Apr 21 '18 at 09:26
  • As depressing as this is, we're all dying. – Adi219 Apr 22 '18 at 12:03
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    Except in the sense that @Adi mentions, would you really describe someone as dying if they had an illness that takes nearly thirteen more years (and who knows how much longer if he hadn’t been Kissed) to kill them off? Usually if you describe someone who has cancer as dying, it means they have terminal cancer, and they won’t be long for this world. Describing a young man who lived another thirteen years with no apparent discomfort as dying would probably be a stretch to most. – Janus Bahs Jacquet Apr 22 '18 at 19:41
  • @JanusBahsJacquet You raise a valid point – Adi219 Apr 22 '18 at 20:47
  • @JanusBahsJacquet " Describing a young man who lived another thirteen years with no apparent discomfort as dying would probably be a stretch to most." That's why my question pointed out that he could have had a terminal illness and then was cured of it when he left Azkaban. Kind of like saying you can get pancreatic cancer, which almost always kills somebody within a year, and then get surgery to remove it, and then live for years after the surgery. That's why I asked if he had one and then was cured. – RichS Apr 22 '18 at 21:10
  • @RichS I think I misread the last bit of your question first time around—your second possibility definitely seems the more likely of the two (though I agree with the answers that it probably wasn’t the case). – Janus Bahs Jacquet Apr 22 '18 at 22:21

3 Answers3

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Probably not - it seemed to be just the effect of being in Azkaban.

It seems most likely that it was the effect of being in Azkaban. Sirius told Harry that Barty Crouch Jr. died in Azkaban, and that many others did as well. He also said Barty Crouch Jr. looked sickly when he arrived in Azkaban, but whether that was due to a separate illness is never mentioned.

“No,’ said Sirius dully. ‘No, he’s not in there any more. He died about a year after they brought him in.’

“He died?’

‘He wasn’t the only one,’ said Sirius bitterly. ‘Most go mad in there, and plenty stop eating in the end. They lose the will to live. You could always tell when a death was coming, because the Dementors could sense it, they got excited. That boy looked pretty sickly when he arrived.”
- Harry Potter and the Goblet of Fire, Chapter 27 (Padfoot Returns)

During a portion of the time while Sirius would have thought Barty Crouch Jr. was in Azkaban, it was actually his mother taking Polyjuice Potion. However, on the first day he was brought in, he certainly wouldn’t have been switched out for his mother, and he seemed to be already affected by being in Azkaban. In addition, he said Winky had nursed him back to health, which wouldn’t be possible if he had a preexisting illness that would be terminal in the wizarding world.

“The house-elf nursed me back to health. Then I had to be concealed. I had to be controlled. My father had to use a number of spells to subdue me. When I had recovered my strength, I thought only of finding my master … of returning to his service.”
- Harry Potter and the Goblet of Fire, Chapter 27 (Padfoot Returns)

Barty Crouch Jr. seems to have healed fully after being taken care of, which wouldn’t be possible if he was dying of a terminal illness. From this, we also know it wasn’t just the effect of taking his mother’s form, since then he wouldn’t need to be nursed back to health. He’d just immediately become healthy again when the Polyjuice Potion wore off.

It seems the most logical conclusion that being in Azkaban was sapping his strength and will to live, and would have been deadly for Barty Crouch Jr. had he stayed. Some people survived being in Azkaban (like Bellatrix, who was imprisoned there for fourteen years and wasn’t sickly when she got out), but many people died from its effects on them. Sirius said Barty Crouch Jr. looked sickly when he came in and started screaming for his mother by the first night - he didn’t seem to be the sort that could survive Azkaban. Once he got out, he escaped the conditions that were killing him, and with care from Winky, he was restored to good health. The “illness” caused by being in Azkaban was cured.

Obsidia
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    If all the inmates are viewed by the Dementors as "dying" then wouldn't breaking prisoners out by swapping people around be tediously easy? – The Dark Lord Apr 21 '18 at 15:04
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    @TheDarkLord yes, if you have someone who is dying and willing to take their place. (And they have to be willing, otherwise they'll spoil your escape by failing to maintain their disguise, the ruse will be discovered and the loophole will be closed) – Arcanist Lupus Apr 21 '18 at 15:36
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    @TheDarkLord The Dementors don’t seem to see all the inmates as “dying”, since they can tell when a death is coming and get extra excited then. There probably wouldn’t be this noticeable difference in their behavior if they considered everyone in Azkaban to be “dying”. – Obsidia Apr 21 '18 at 20:34
  • @Bellatrix But you're saying that Crouch Junior was dying (like all the other prisoners) because of the effects of Azkaban, right? Unless I misunderstand your point. – The Dark Lord Apr 21 '18 at 23:18
  • @TheDarkLord Sort of - I’m saying Azkaban affected him to the point where he was dying of its effects on him, like many prisoners do. However, when and even if they start dying from its effects varies. Several other prisoners weren’t doing well in Azkaban but weren’t anywhere close to dying, like Bellatrix and the other escaped Death Eaters. – Obsidia Apr 22 '18 at 03:15
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    @TheDarkLord I love how Bellatrix, Voldemort and a fake Remus Lupin are debating whether Barty had a terminal disease – Adi219 Apr 22 '18 at 12:06
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Being in Azkaban is a terminal illness.

In spite of opposition from many wizards, among them experts on both Dementors and buildings with Azkaban’s kind of Dark history, Rowle carried out his plan and soon a steady trickle of prisoners had been placed there. None ever emerged. If they were not mad and dangerous before being placed in Azkaban, they swiftly became so.

It was only when Diggory went to visit that he realised exactly what conditions inside were like. Prisoners were mostly insane and a graveyard had been established to accommodate those that died of despair.

Back in London, Diggory established a committee to explore alternatives to Azkaban, or at least to remove the Dementors as guards. Experts explained to him that the only reason the Dementors were (mostly) confined to the island was that they were being provided with a constant supply of souls on which to feed. If deprived of prisoners, they were likely to abandon the prison and head for the mainland.

Azkaban by J.K. Rowling

I would hazard that Barty Jr. had been in Azkaban so long that he was succumbing to the fate that all of prisoners who entered fell to.

Skooba
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No, Barty Crouch Junior wasn't dying.

There's no indication that Barty Crouch Junior was dying at all.

The reason the Dementors viewed Crouch as a "dying person" was because of the Polyjuice Potion.

"They came to visit me. They gave me a draught of the Polyjuice Potion, containing one of my mother's hairs. She took a draught of Polyjuice Potion, containing one of my hairs. We took on each other's appearance."
(Goblet of Fire, Chapter 35, Veritaserum).

I disagree with NominSim's theory that Barty Crouch Junior was already dying. It makes no sense for his parents to engage in a daring and highly risky escape attempt if they believed that he was already dying. Their endeavour would have been futile if Crouch Junior's death was imminent.

The only person who was "dying" was Crouch's mother. When Crouch Junior took the Polyjuice Potion he took on his mother's physical form - including her illness. As far as the Dementors were concerned Crouch Junior was "dying" because he had taken the form of the body of a dying woman. They detected one dying person (Mrs Crouch) entering and the same dying person (or so they thought) leaving. The whole statement about a dying person leaving is told from the Dementors' point of view, which is incomplete because they are blind. It isn't intended to tell us anything about Crouch Junior himself.

We know that people who take Polyjuice Potion take on the deformities and disabilities of their targets. Thus Crouch Junior's leg shrunk to become Moody's stump and Hermione inherited Harry's bad vision.

"Harry, your eyesight really is awful," said Hermione, as she put on glasses.
(Deathly Hallows, Chapter 4, The Seven Potters).

In the same way, Crouch took on his mother's illness when he took on her body. When the Polyjuice Potion wore off he no longer had that illness.

It's not the right place for me to fully answer the linked question. But I would prefer David Stratton's answer, which says that Mrs Crouch died because of the limitations of the Polyjuice Potion. In other words, if you're dying when you take the Potion you will still be dying, even if you're taking possession of a healthy person's body. Otherwise Polyjuice Potion would be a means of cheating death or achieving immortality, if the old and the frail permanently steal the form of the young and the virile. I think that it's fair to assume that the healthy can (temporarily) assume the form of the dying but that the dying cannot regain their health by taking the form of the healthy.

The Dark Lord
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    What still nags at me is that if Mrs Crouch was taking the potion up until she died and was buried with people thinking she was her son... That'd have meant they'd discovered her death and buried her in less than an hour given you're supposed to take PJ every hour. That then possibly makes it a rather daft plan given the risk that small window offers up for suddenly finding a rather important figure's wife in the cell... Unless of course, if you die while using PJ you just never change back... which might complement David Stratton's theory... – Jon Clements Apr 21 '18 at 13:10
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    @JonClements a) the Dementors are blind; b) yes, I believe that if you die in a Polyjuice form then you retain that form in death. – The Dark Lord Apr 21 '18 at 13:16
  • Indeed the dementors are blind but does their description sound like they'd perform burials? :) So I'm guessing that if you die while PJ'd - you don't change back... but not sure if there's anything canonical regarding that... Of course - it could just be JKR failling at logic/math again :) – Jon Clements Apr 21 '18 at 13:19
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    @JonClements "The Dementors buried him outside the fortress, I watched them do it." Sirius Black. So the only ones who would've seen the body close up were the Dementors. – The Dark Lord Apr 21 '18 at 13:27
  • Ahhh... okay... fantastic quote. Somehow it doesn't seem to sit too comfortably with She was buried under my name, and bearing my appearance. Everyone believed her to be me... – Jon Clements Apr 21 '18 at 13:43
  • @TheDarkLord " if you're dying when you take the Potion you will still be dying, even if you're taking possession of a healthy person's body." Which supports the theory that Junior was already dying. If he was dying when he took the potion, he would still be dying after he took it. – RichS Apr 21 '18 at 14:01
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    @RIchS Except it seems he wasn't dying in a terminal sense... more just a probably wouldn't have lasted much longer where he was but once out of the atmosphere of Azkaban - he was able to recover... – Jon Clements Apr 21 '18 at 14:05
  • @JonClements He recovered partly due to help from a female elf named Winky who was once in the Crouch household. – RichS Apr 21 '18 at 14:08
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    @RichS Indeed... so as this answer states - it's more likely the dementors sensed the "dying" person as his mother whose form he was in at the time... as opposed to reading it as Junior was dying whether or not he got out of the place. – Jon Clements Apr 21 '18 at 14:10
  • @RichS That quote was an explanation of why Mrs Crouch died. If Crouch Junior had been dying when he took the Potion then he would still be dying after. But he wasn't so he didn't. Apart from anything else, if you have a terminal illness and still haven't died after 11 years can it really be said to be terminal? – The Dark Lord Apr 21 '18 at 15:01
  • @TheDarkLord Alzheimer's is a very slow acting terminal illness. My grandmother had it for 9 years before it finally killed her. Not saying Barty Junior had Alzheimer's (that would be a weird twist), just wondering if he had something like cancer. If untreated, he would die in prison. If he was outside prison, he could be treated and nursed back to health. – RichS Apr 21 '18 at 15:25