Fiona's Mother

[Christmas Chief]

The idea Fiona's mother died in a V.F.D.-related scheme might give the captain a reason to lie about the nature of her death; however, as mentioned previously in this thread, Lemony's narration later on does indeed seem to imply Widdershins really does believe her to be the victim of a manatee accident. Perhaps he was misled somehow, whereas Fiona was inclined to do further research? As you note, there are numerous possibilities, supplied mainly by the fact we don't get any clues concerning the accident after TGG.

[Charlie]

Well presumably either there was a manatee accident of some sort at some point, or that is a VFD cover up phrase for something else. Thursday was said to have died in this fashion, but it is then revealed that he was in fact alive. Interestingly, we never get to know what was done at Anwhistle Aquatics (unless I am forgetting something), and I have a few theories.
Lachrymose Leeches: It is said in WCTBATH that Lachrymose leeches cannot be tamed. Perhaps this was the purpose? It also ties in well with Ike and Josephine dying from leech attacks. Gregor was said to be a volatile man, and this ties in well with wanting to tame leeches
Stricken Salmon: Okay so the Stricken Salmon live in the Stricken Stream, which leads to the GG which is below AA. They were said to be able to smell smoke or something... I don't know, it kinda works
Submarine Manufacture: Perhaps VFD submarines were made here. This makes the name more like "Anwhistle [Mechanical] Aquatics". We never have any other evidence of where the submarines might be manufactured, and the GG seems like a good enough place to store Submarines. It also explains why Fernald wanted to burn it down, to spite his submarine loving Stepfather.
Taming Manatees for VFD: I don't know, "Very Fat Dugongs"? Maybe they were used for whatever reason at AA, and Fiona's mother worked there. This might work as a manatee accident, which was in fact, not an accident, as it was arson. Mrs. Widdershins could have escaped, and met up with Lemony, explaining why he says Cpn. Widdershins was wrong to think she died there. I don't know

On Mrs. Swim. She is probably not Kit, as then Lemony would know that she had been alive at that point. She could have been Mrs. Widdershins I guess. Same with the Duchess. She was probably not Esme, as it would not make sense that Lemony had her in his boot. No wait, perhaps I have been looking at it wrong this whole time. What if Mrs. Swim was a villain, and she was in Lemony's boot because he had either captured her, or she had snuck into his boot, much like the orphans in THH-TCC. I don't know about her either. Who knows, not me, that's for sure

[Christmas Chief]

Well, Anwhistle Aquatics is called a "research center," which narrows down the possibilities somewhat. I don't believe we're given any details on the precise nature of the research, though.

[Dante]

Except that they researched the Medusoid Mycelium. If that spread out of control due to any slight accident, everyone in the research centre and rhetorical advice service would be in incredible danger. Perhaps enough danger that a volatile person would think it was safer to burn the whole place down to cleanse it.

[TheAsh]

I have always assumed Fiona's mother and Mrs. Widdershins is Miranda Caliban.

There are three reasons for this:
1) The F names: Fiona, Ferdinand, Friday. (I know her father's Thursday, but we can assume the name was by mutual agreement.)
2) The Manatee accident excuse. If I recall correctly, Ishmael just told Miranda to tell her daughter her father had died. Miranda is the one who makes up the Manatee excuse. (A further possibility is Ishmael thought up the excuse, and he took Miranda onto the Bathyscape, and used that excuse for Captain Widdershins as well. A third possibility is the excuse is Thursday's invention: He told Widdershins his ex-wife died, and Miranda used the same excuse (Keep in mind he apparently did not tell Kit that his wife was on the Island, indicating that he is hiding something.) Either way, the result is the same: The excuse is used for some family connection.)
3) Captain Widdershin's closeness to Olivia.

[Hermes]

I think this is a theory we are meant to think of, but is not, in the end, true. When we first hear of the manatee, it's quite plausible that the two manatee stories are versions of the same incident; Captain Widdershins and his wife were separated in an incident involving a manatee, and each concluded the other was dead. Add to that the name 'Friday', and the VFD habit of having three-child families, and we get a plausible history in which Friday is the half-sister of F and F. But then we find that there was really no manatee incident, and in fact F's father, who is clearly not the captain, has deserted his wife and daughter. So it turns out that it is, like so much in The End, not the same story but a parallel, in the same style as those in Ishmael and Olaf's stories - and there is a further parallel when Friday, like Fiona, deserts the Baudelaires out of loyalty to her family.

It's possible, with some ingenuity, to make the stories still connected, but you have to add complications. Are you taking it that Miranda married Thursday after leaving the captain? But the captain seems to have no awareness that she left him - he simply thinks she is dead - and if she married Thursday while the captain believed she was dead, and so no actual divorce has happened, it wasn't a real marriage.

[TheAsh]

I never assumed it was the same incident. i assumed it was the same phony excuse.

My basic theory is that Miranda married Thursday, who got shipwrecked. Or possibly Miranda deserted him. Miranda married Widdershins. Miranda got shipwrecked. Miranda remeets Thursday, and remarries him, has a third kid. Thursday deserts Miranda, like she once did to him.

The legality of the marriage is a non-issue, who cares? Daniel Handler isn't too concerned about living in sin.

[Dante]

Like Hermes, I think Miranda Caliban being Fiona and Fernald's mother is a theory we are meant to suspect; but, if intended to be the truth, it's insufficiently communicated - and arguably disproven using direct evidence.

First, though, I think we should remind ourselves exactly what is said about Fiona's parents, particularly in her own words:

"The original second in the crew of two was Fiona's mother, but she died in a manatee accident quite a few years ago."
"I'm not so sure it was an accident," Fiona said.

-TGG, pp. 42-43

"My father moved away."

-TGG, p. 291

[Captain Widdershins] was wrong about his wife's death, because as Fiona suspected, Mrs. Widdershins did not die in a manatee accident.

-TGG, p. 310

So, the overall indication is that there really was an incident involving a manatee, Fiona was a witness to it or at the very least closely involved, and Captain Widdershins probably isn't aware of the truth of the situation. Additionally, if Thursday was Fiona and Fernald's father, his departure from their life was, at least, unexciting; or, considering that Fiona must have been too young to remember him (since she was a baby at the time Captain Widdershins joined the family), not of such notoriety that she could be fed a false story in perpetuity.  So all of these factors must be taken into account by any theory attempting to link the Calibans to Fernald, Fiona, and Widdershins.

And that brings me to the most important point, one so glaringly obvious I can't believe we never noticed it before, which is that we can more or less conclusively disprove that Miranda Caliban is Mrs. Widdershins because the Baudelaires know what both of them look like:

Klaus looked at what his sister had given him. It was a photograph, blurred and faded with age, of four people, grouped together like a family. [...] On the other side of the captain was a woman who was laughing as hard as the captain, and in her arms was a young infant with a tiny set of triangular glasses.

-TGG, p. 267

Now, it is possible to get around this, if you want to argue that Miranda Caliban had aged sufficiently to alter her appearance and that the blurring and fading of the original photograph was such as to partially obscure her facial features. But neither of these points are indicated; and furthermore, there's no positive indication of a family resemblance, either. So this starts to look very much like an enormous coincidence.

[Optimism is my Phil-osophy]

Very good Dante. I had never seen the accident involving this marine animal as having actually happened. I thought there was no accident. Was it possible that the "manatee" in question was a type of BB in development? I mean, when that woman who was Mallahan's ancestor killed a strange animal, many said it was a manatee. Did Captain W.'s wife be swallowed, leading him to believe that she was dead, but then she came out alive, showing that it was possible to be transported through the beast's mouth? Was the mysterious woman who went to GG actually Captain W's wife? And was it possible that it was because of this encounter with her that he realized that the ferocious animal in the form of a question mark was possible to be controlled by someone? And is that why Captain W preferred to take his chances with the TGU instead of running away? After all, he had shown fear of the submarine. But he would not be afraid if he believed that the entity that submerged the water was the animal, and if he knew that the animal could be controlled by someone, (not by means of a whistle, but by a qualified trainer).

[Hermes]

Very good point about the photograph. That seems to settle that particular theory.

It remains possible, as people have occasionally suggested, that Thursday is F and F's father, making Friday their half-sister on the father's side; but while nothing rules this out, nothing makes it likely either; it doesn't explain the manatee, since the two alleged incidents must have happened to the two ex-partners long after their separation. So I prefer to believe that F and F's father was called Fagin.

The captain's words suggest that Mrs Widdershins was a member of the crew up to the time of her death, which in turn suggests she died (if she did) when he was nearby; it doesn't look as if the incident can be wholly invented, as Thursday's was. it's not clear, though, whether he is wrong about her being dead, or just about whether it was an accident; and indeed, as JL suggests, he may also have been wrong about whether it was a manatee.

[Glittery666]

I assumed the manatee accident thing was code for "we don't talk about it."