One day, around 1897, a young, single woman, Emma Eckstein (1865-1924), aged 32, had the bad luck to enter Freud's office. Freud quickly diagnosed her as a hysteric and started the treatment. Allegedly, as the story goes, her symptoms could be removed by an operation.
Subsequently, Freud asked his bisexual lover, doctor Wilhelm Fliess from Berlin, to operate on Emma. Fliess came, operated, and went home.
The operation was a total failure. Emma bled constantly and almost died. Other doctors were called that saved Emma's life.
This is the Freudian version of what happened. Most of it is true, except the reason for the operation and what Emma was operated on.

This is what happened. Having diagnosed Emma as suffering from hysteria, Freud started his sexual cure that involved the use of hypnosis, drugs like cocaine and morphine, and last but not least, Freud's, and Freud's partner in crime, Fliess', oral and genital equipment. The treatment didn't cure Emma, but, not unexpectedly, since Freud refused to use any contraception, made her pregnant.
There's little doubt that also Fliess played an active role in Emma's sexual "cure". No wonder that when Freud called - after all, it wasn't certain whose sperm it was that impregnated the woman - Fliess came to Vienna to perform an abortion - free of charge.
Acting as an abortionist was a risky business. At the time, abortions not only were illegal but also carried a serious - five years' - prison sentence. Moreover, both doctors, since Freud participated in the procedure, would lose their licenses. This had to be a clandestine operation.

In his psychopathological book, Freud recounts an alleged occasion when, Two men, an older [Freud] and a younger one [Flies]… were exchanging recollections. (1) The older asked the younger about, the place … that was called Enna in antiquity, and pointed out that, Enna was also a substitutive name.(2)
Knowing Freud’s penchant for word puzzles, it is not difficult to realise that Enna stands for Emma. This is how Freud recounted the conversation.
The younger man said, I’ve suddenly thought of a lady from whom I might easily hear a piece of news that would be very awkward for both of us. And the older replied, That her periods have stopped?(3)
Why would this news be awkward for both Freud and Fliess? The answer is obvious, Both of them had had unprotected sex with the lady in question that is Emma, either one-on-one, or, more probably, in tandem, and as a result, neither of them could be certain which of them was the sperm donor, aka father, which would explain why Fliess performed the abortion free of charge. Apparently, the anecdote is a throwback to the botched abortion.
How can we be sure that Freud is talking about his former lover? In his letter to Fiiess, of August 7, 1901, Freud explained to him, my "Everyday Life" ...  is full of references to you - manifest ones …  and concealed ones.

(1) SE 6, p. 30.

(2) SE 6, p. 31.

(3) SE 6, p. 11.

(4) Freud, Sigmund, The Complete Letters of Sigmund Freud to Wilhelm Fliess, 1887-1904, (1985, p. 447).

As a general practitioner, Fliess had never performed an abortion but it didn't stop him from trying. The operation was a partial "success" since Fliess managed to kill the fetus in Emma's womb, but didn't manage to abort it.  Soon thereafter, Fliess went home to Berlin. In the aftermath of the botched abortion, Emma started to bleed copiously.
In his dream book, Freud hints at the botched abortion. While walking with Fliess, a little girl asked Freud about the way. I remarked to my friend, wrote Freud, it is to be hoped that when she grows up that little girl will show more discrimination in her choice of the people whom she gets to direct her.
Now comes another hint, Freud writing: I caught sight of a door-plate bearing the words Dr. Herodes. And, since King Herod committed mass infanticide, this is an obvious allusion to Fliess killing the fetus.
As if this wasn't clear enough, Freud added that he hoped, that our colleague does not happen to be a children’s doctor.*
* SE 5, p. 443. 

One day, one of the doctors, pulled out from Emma's womb at least half a meter of gauze that Fliess left behind. Then, came the flood of blood *
A piece of bone, (the size of a heller, or a penny, about 2 cm in diameter), and two bowlfuls of pus followed. Of course, a bone that big couldn't have come from Emma's small nose. And there's not enough space in the nasal cavity, for this amount of gauze and pus.
On the other hand, as any abortionist knows, the uterus cavity, when inhabited by a fetus, has lots of space. And, such plentiful bleeding can only come from a big blood vessel not found in the nose.
* Schur, (1966, p. 56).

But what happened next was even more astonishing. In the aftermath of the massive bleeding, a foreign body * came out. It wasn't a body of a foreigner, but the dead body of, Freud's own, rotting fetus.
Significantly, in this context, Freud mentioned, my child of sorrow.* Was he talking about Emma, or the dead Freudian fetus?
* Schur,Freud: Living and Dying, (1966, p. 57 & p. 58).

Even in the aftermath of her botched operation, Freud still insisted that her bleeding and pains were hysterical, and "treated" her for her problems. What kind of treatment could Freud offer the ailing woman? Unfortunately, for Freud, her state precluded sexual treatment. Thus, Emma was given morphine*, (not mentioned in Schur's book), possibly together with cocaine, Freud's standard (non-sexual) remedies.

Freud's affection

In the letter of May 4, 1896. Freud revealed that their relationship was not entirely professional. In the sanatorium, he wrote, since I did not come during the night, she renewed the bleedings, as an unfailing means of rearousing my affection.** There’s no doubt what kind of affection Emma was craving from her lover, just like there's no doubt that Freud was insane.
* Schur, Max, Freud: Living and Dying, (1966, p. 63).
** Freud, Sigmund, The Complete Letters of Sigmund Freud to Wilhelm Fliess, 1887-1904 (1985, p. 186).

Notably, Emma's operation took place in Freud's own home. She remained there for several days until she was well enough to be moved, at Freud's expense, to a private sanatorium. As Freud revealed one of the doctors attending to Emma admired, an etching The Isle of the Dead by Böcklin* on the wall of his apartment.
The fact that the operation was performed in Freud's home - with the assistance of Freud's wife (!) who served Freud a glass of cognac - and not in a hospital - is the best indication that it was illegal.

Illegal abortion

Even though Emma almost bled to death, neither Freud nor his doctor friends ever considered moving her to a hospital. After all, the "partners in crime" were acutely wary of the criminal character of their actions.
The 1852 Austrian legislation criminalised abortion; both the woman and the abortionist faced up to five years in jail. Not unexpectedly, the perpetrators of Emma's ordeal, were more afraid of the legal consequences of their actions than of signing Emma's death certificate.
* Freud, (1985, p.113). The letter to Fliess of March 4, 1895

In the aftermath of Emma’s haemorrhage, Schur claimed that the operation was performed in the patient's home instead of in a hospital, where the wound could have been widened (as it was later). (1)
(Fact check: Schur was lying. The operation was performed in Freud's home.) Moreover, Emma's wound [was] curetted. (2)

Abortion

By now any doctor, also Schur, should realize that Emma was having an abortion. According to the medics, [h]ealth care professionals perform dilation [widening} and curettage [scrapping] to diagnose and treat certain uterine conditions — such as heavy bleeding — or to clear the uterine lining after a miscarriage or abortion. (3)
Now, the widening of the opening, and curetting of Emma's wound starts making sense.
(1) Schur, (1972, p. 81).
(2)  Schur, (1966, p. 57).
(3) Mayo Clinic. Dilation and curettage (D&C). Online. 10.10.2024.

In the aftermath of the botched abortion, in the letter to Fliess, of April 26, 1895, Freud mentioned Emma, referring to her as, my tormentor and yours.* There's no doubt that to make this kind of accusation, he must have been insane. Emma was a victim, and the two mad doctors were the tormentors.
But did Freud really write those words in the German version of the letter? According to Peter Gay, a biographer who also had unfettered access to Freud's correspondence, Freud wrote something totally different, referring to Emma as, my incubus and yours.**

Incubus

There’s a big difference between tormentor and incubus. An incubus is a demon in male form that attempts to have sexual intercourse with women in their sleep.
Why would Freud call Emma an incubus, while the female demon that seduces men is called succubus?
Since Emma was a female, it is apparent that it was rather both Freud and Fliess who could be classified as incubi, a couple of demons taking advantage or a helpless woman, no doubt subjected to Freud's standard aphrodisiac cure with cocaine.
Without a doubt Freud knew the difference between a succubus and an incubus. So why would he refer to incubus when talking about Emma? He wouldn't. Instead, it is more likely that to hide the sexual nature of the statement, the biographer deliberately distorted what Freud had written.
In any case, even in Gay’s version, Freud hints at Emma being engaged in a sexual act with her doctor, which only confirms the fact that Freud, and most probably also Fliess, were Emma’s seducers.
* Freud (1985, p. 127).
** Gay, Peter, Freud: A Life for Our Time, (1988, p. 85). 

Dr Schur lied about the true nature of the operation, but he had no other choice if he wanted to have his revelation published. At the time, the Freudian mafia was censoring all news that could soil Freud's saintly image.
Thus, as it appears, to bypass the censorship of Anna Freud, Schur claimed that the operation was on Emma's nose rather than on her uterus. Even so, he still wanted the truth be known, since his German transcription of the original letters -and obvious hint - mentions foetos* rather than foetor.
* Schur, (1972, p. 59).

Notably, Schur's English version of the statement doesn't mention the word foetus. Apparently, it was "lost" in translation. Rather, it states that, a foetid odor set in along with an obstacle to irrigation.* (N.B. he word "odor" doesn't appear in Schur's German transcription.)
No doubt, the Latin experts, will point out that fetus in Latin is spelled foetus rather than foetos. But maybe they are missing something.
* Schur, (1972, p. 56).

In the Latin declension table, the accusative masculine plural of foetus is foetos, which indicates that there was a male foetus. and that there could have been more than one foetus that was aborted.  Thus, the alternative English translation would get an even more ominous meaning, suddenly an obstacle and the fetuses appeared during irrigation*.
Were there two fetuses?  Was Emma carrying twins? Or maybe there was only one foetus, and Schur, an apparent pro-lifer, chose the accusative form of the foetus to “accuse” Freud of, an at the time criminal, act of infanticide.
* Schur, (1972, p. 59).

Writing to Fliess, on June 12, 1895, only a couple of months after the botched operation, as Eissler in his article recounts, Freud mentioned sending a six-month-old fetus on a dance, (1) without specifying its sex.

Fetus of a girl?

On the other hand, in his letter to Fliess, on  June 12, 1895, Freud mentioned, sending a six-month fetus of a girl to a ball. (2)
Since the translations differ, the only piece of information that is certain is the fact that Emma's aborted fetus was six months old.
(1) Eissler, KurtR., A Farewell to Freud's "Interpretation of Dreams" - I wish., American Imago, Vol. 42, No. 2 (Summer, 1985), pp. 111-129., (p. 126).
(2) Freud,  (1985, p. 131) 

In his psychopathological book, Freud recounted a case of a married woman, Frau X., with three children who, with her husband's consent, had an abortion.
Most of the statement is a brazen lie. There was never a Frau X., but there was the single Emma without children. But there was her de facto, husband, Freud.

Fliess having a sex change

How do we know Freud was talking about Emma's abortion?
We know that thanks to Freud's hint in his psychopathological book.
Thus, Freud recounts that Frau X. regretted the abortion that, as Freud revealed, had been started by a woman quack but had to be completed by a specialist *.
Except for the claim that the abortionist was a woman, the other details are correct. Also, Emma's abortion, just like X's, was performed in stages; started by Fliess, was continued by several of Freud's doctor friends.
As is apparent, in this manner, Freud was recounting Emma's botched abortion performed by Fliess.  
* SE 6, pp. 183-184

Nine years after her ordeal, in 1904, Emma wrote a book about child-rearing, in which she included a letter to an imaginary child (of unspecified sex and age).
Notably, writing to Dr. M. Furst, in 1907, Freud mentioned, the charming letter … which Frau Emma Eckstein quotes as having been written by her to her son when he was about ten years old.
No doubt, since he recounted the imaginary son's age and sex, Freud knew whose child Emma was writing her letter to, Had Emma's male fetus survived, in 1904, the boy would have been nine years old.
Masson, J. M., The Assault on Truth, (2003, pp. 248ff). 

There's a proof of Emma's relationship with Freud In her correspondence with Freud.
Thus, writing to Emma, on November 30, 1905, Freud coldly stated, I am supposed to have offended you by denying you the qualities that would attract a man; the other time I must have offended you by explaining to you how it happened that in our relationship love did not appear.*
There was no love, but there was unprotected sex. No wonder that Emma fell pregnant, and subsequently had her child aborted. Notably, while their relationship went on for over ten years (since at least 1894), Freud was allegedly happily married to Martha Bernays fathering, at least some, of their six children.
* Masson, J.M., The Assault on Truth, (2003, p. 257).

The names of the doctors participating in Emma’s episode were revealed in full in 1985 in the so-called complete correspondence of the two “partners in crime”. None of the doctors, except for Weil - assuming it was the right Weil that was identified - was an ear and nose specialist.

• Dr Wilhelm Fliess (1858-1928)
  According to, The Origins Of Psycho-Analysis, Letters to Wilhelm Fliess: Drafts and Notes 1887-I902, published in 1954, and edited among others by Freud's daughter, Anna Freud, Fliess was a Berlin physician and biologist (1) and not an E.N.T specialist. Notably, just like Schur, although 17 years later, the editor of Freud’s letters to Fliess, claimed that Fliess was, a successful ear, nose, and throat doctor in Berlin. (2)

• Dr Robert Gersuny (1844-1924)
  Gersuny was a well-known plastic surgeon. (3) Gersuny also invented several gynecological surgical procedures which are now commonplace. (4) As a matter of course, calling upon a gynaecologist to operate on a patient’s nose is not a good idea.

• Dr Ignaz Rosanes (1857-1922)
  According to Masson, Ignaz Rosanes, an ear, nose, and throat specialist in Vienna, … was a boyhood friend of Freud. (5) In 1886, Freud and Rosanes worked together at the Institut Max-Kassowitz. Rosanes worked in the surgery department. (6) Rosanes was a general surgeon, not an E.N.T. specialist.

• Karl Gussenbauer (1842-1903)

Gussenbauer was professor Billroth's (1829-1894) successor in the “Chirurgische Klinik” in Vienna . He was a brilliant Austrian surgeon, a Pioneer in Modern Pancreatic Surgery, but not an E.N.T. specialist. (7)

• Dr Moriz Weil  (d.o.b., d.o.d. Unknown)
  According to the editor of Freud's Fliess letters, Weil was an E.N.T. specialist. (8).
  
  

None of the doctors had a problem participating in an illegal abortion, taking this knowledge about Emma's abortion with them to their graves.
At least one of them, Gersuny had been performing abortions on other occasions. In the letter of January 24, 1895, Freud encouraged Fliess to practise with Gersuny before attempting it himself. How would it be if you first experimented on the preparation jointly with Gersuny? Freud wrote. Fliess chose not to, with a catastrophic result.
(1) Freud, Sigmnd, The Origins of Psycho-Analysis: Letters to Wilhelm Filess, Drafts and Notes, 1887-1902, (1954, p. ix).
(2) Freud, (1985, p. 1).
(3) Freud, (1985, p. 106). 

(4) Gersuny: German Wikipedia, https://de-academic.com/dic.nsf/dewiki/515006, 20.07.2022.
(5) Freud, (1985, p. 118).
(6) Bonomi, Carlo, The Cut and the Building of Psychoanalysis, Volume 1, (2015, p. 32).
(7) Schnelldorfer, Thomas et al., Carl Gussenbauer: Pioneer in Pancreatic Surgery, World J. Surg. 27, 753–757, 2003.

(8) Freud, (1985, p. 126).