Freefall/WMG

The Sqids are survivors from the Dalek war.
In the Doctor Who episode "The Evil of the Daleks", many Daleks were infected with the Human Factor, which made them more Human and less Dalek in mind. What the episode doesn't reveal, is that some of them escaped from Skaro, and upon arrival, destroyed all their Dalek technology to avoid detection.

During the following centuries, they evolved, but retained some of their Dalek untrustworthiness, before being encountered again by humans.

Dr. Bowman is on Jean and is responsible for most major events of the comic.
This is a fairly common opinion on the Freefall forums and is considered fairly probable considering that the robots are using his brain design. Whether he caused Florence to be thawed out at Jean is debatable.
 * Sam is the one who gets Florence thawed out as evidenced here.
 * Are you sure about that?
 * Another wild theory concerning Dr. Bowman is that he is actually one of the uplifted chimps that Florence mentioned, he has been described as a sociopath and we have no idea what he looks like.
 * The really fun version of the 'chimp' theory is that Bowman is the original * computer simulation* of an uplifted chimp's brain.
 * The chimps were created a hundred years previous but it has been implied that life extension pills are available over the counter.
 * Heck, once someone suggested that Sam was really Dr. Bowman, seriously.
 * The mustache! The lab coat! It all makes sense now!
 * What about the Robo-Captain? He is a human (almost certainly gravely injured) on a robotic frame and helps other robots (and Florence, once he meets her) found an AI society.

Dr. Bowman IS Jean, and is responsible for most major events of the comic.
OK, this is a completely insane one inspired purely by the existence of a character named Bowman Jean in the Star Ocean series. Dr. Jean Bowman is a Genius Loci created by a freak accident during the terraforming process- as such, the entire planet is an incredibly intelligent life form. When the first robot factory ships landed and were damaged, Jean came up with his brain architecture and arranged for the factories to be rebuilt using it to create more intelligent robots. The Bowman's Wolves would have to have come later though, after he got a job with Ecosystems Unlimited, presumably by having a human assistant pose as the real inventor.

Florence is doctor Bowman
She's been referred to as "Florence Bowman" on some occasions. Besides, according to the Fanon of one White Pony, she's been his (WP's) lover since times immemorial. Obviously she assumed the identity of a genetic scientist and created the Bowman wolves to explain her own existence.
 * When was she referred to as "Florence Bowman"?
 * Recent Cross Time Cafe strips suggest that it's something of a Reincarnation Romance thing.
 * Which is irrelevant. CTC events are totally non-canon to the respective "source" webcomics. There's even a disclaimer at the bottom of each CTC strip page to that effect.

What will happen to the A Is later.

 * The Robots will figure out a way to bypass their safeguards and overthrow the humans as Jean's dominant species, not many people have actually suggested that as the robots are mostly on humanity's side.
 * And robots are arguably already the dominant species on Jean seeing as they vastly outnumber the colonists.
 * They will do so by creating a robotic bureaucracy in which robots who implement orders are insulated from robots who receive orders by at least one level of middle management that doesn't know which orders originated from humans. Meanwhile, they will ensure that life on Jean (and any other planet where the system spreads) is pleasant and entertaining for its human inhabitants and that only meticulous investigation would reveal that humans aren't actually in control.
 * The robots will peacefully convince the humans to give them equal rights, unfortunately that seems unlikely as most of the people in power seem to think of A Is as appliances.
 * They will leave Jean and found their own colony, away from humanity.
 * Florence did suggest that robots who have undergone neural pruning do terraforming work in some of the uncolonized areas of Jean as an alternative to being scrapped.
 * Getting 100s of millions of robots on a colony ship would be extremely expensive, though they could probably colonize an unihabited planet or moon in the same system.
 * The robots will continue on until they create their own fully functioning sub-society which functions within the bounds of their existing role in human society, with their own robot laws and the beginnings of their own culture. However, since they will still not be able to harm or disobey humans, and human laws thus take absolute precedence over their own, by the time they figure it out it will be obvious to the humans that this is not a threat, and they will be allowed to do it peacefully. Also, it will rain cotton candy and everyone will live happily ever after. Alternately, the humans will notice the robot society, freak out because they sure as hell weren't expecting it, and take drastic and disastrous action to try to keep everything "under control", despite the fact that the robots could still not harm or disobey humans and human laws would still take precedence over their own even if the humans did nothing.
 * Robots prefer to follow human instructions, and not harm humans. They are not Three Laws Robots. They are not required to follow laws. There are known workarounds suspected, although not tested, and Florence is based on the same AI and able to operate well outside of her limitations. There are greater methods known.
 * I think that must vary from robot to robot. Perhaps, taking it in the logical direction, the older they get (and thus the further Dr Bowman's self-improvements progress) the more they become able to make their own decisions rather than just listen to humans. There are some robots we've encountered who couldn't even picture the concept of disobeying an order, and Max Post mentions that he could walk up to a robot on the street and tell it to pull its own head off, but Sawtooth actively thwarts his expiration date, the junkyard robots are not doing their jobs, and Helix has stated that he chose to work for Sam because he's happier if he doesn't have to worry about his safeguards. Whatever the case, the first law is in full effect, and that's the important one. Asimov's robots also had loopholes that said they could hurt one to save many; the only difference is that this time the programmers were sloppier about what constitutes a threat. Also, remember that Florence is not subject to the laws the same way they are; her safeguards were made to imitate theirs and hardly do anything at all; she can ignore them anytime she feels the need, even the big one.
 * No she can't. Florence must obey the second law. Yes, being intelligent and free-willed, she can rationalize her way around her safeguards, when she wants to. But she can't simply ignore them.
 * I think we can all agree that we would all like to see The Mayor, Mr. Kornada, and all the Obstructive Bureaucrats and Corrupt Corporate Executives that control Planet Jean sent packing, at the very least.

The AIs use different metrics than words to determine gender.

 * The reason for the lie is obvious. They know that selecting genders and electing to make robot children scares the crap out of most humans from off-planet. The robots are Bowman-based, and thus empathize very well with humans. They know that if humans know what makes them 'male' or 'female', they'll try to alter disable all the 'female' robots in the misguided assumption that this will prevent them from reproducing. If the actual attribute is part of the neural net, this will almost certainly result in the robots being permanently destroyed and a backup used instead. 'Male' robots keep to fewer words (although not always within the criteria they describe), and 'females' contrawise so it's not a complete lie.
 * I don't see why humans would carry out a robot Gendercide unless the particular humans doing so were impulsive, irrational idiots (which can't be entirely ruled out). Since robots don't have actual reproductive organs, there's no reason why producing a robot child would require a male and a female robot. Same-sex robot couples could do it, individuals of either sex could do it unassisted, a group of robots could all make a kid together, etc. One would assume anyone with a passing knowledge of robots would know this.
 * Considering we already have humans that stupid in the form of Mr. Kornada, the possibility of a misguided gendercide seems very likely.

Florence has SRMD.
Evidence: Looks a lot like a Paragon Hoffnung Artificer to me.
 * Wants to eat the sun and feed it to people.
 * Calls planetary scale plans "medium sized ideas".
 * Will not dissect Ridiculously-Human Robots For Science! because it´s "impolite".
 * Considering her background in FTL physics I'd say she's more like a cautious Navigator (but definitely a Hoffnung).
 * Dvorak is probably a Staunen Artificer while Dr. Bowman could be a Hoffnung Progenitor.
 * And now Dvorak has proposed destroying a universe to store his tweets.

Florence is either the inspiration for, or the Reincarnation/Alternate Universe version of Sagrim-Ur.
(Sub)Species? Check. Inquisitive, science-inclined? Double check. (See WMG above.) "Honor Your Territory in All Things." (I. E. prevent neglect and damage)? "" ENGINEERING. KEEP OUT. . Sam & Helix. That means YOU.""

Check. FF online since 1998. WtF released in March 2005. Check(?)

Sherlock Scan at Kinetic Chemicals: How Did He Do It?
In 1822, Florence arrives at a chemical supplier to purchase reaction mass. The proprietor is initially discombobulated, but soon takes her presence as a challenge ... and makes three correct deductions.

1. Florence is a gravitational engineer.

2. Florence arrived on the starship Asimov.

3. Florence works for Sam Starfall.

So far, This Troper has come up with partial theories for 1 and 2, but almost nothing for 3.

Gravitational Engineer: Her language betrays an engineer's mindset and vocabulary, and "we" implies that she is working on the ship delivering the reaction mass. (But how do you get gravitational from that?)

Arrival on Asimov: How else would she get there? There are pretty severe penalties for creating something like her.

Working for Sam: This is the stickiest bit -- all I can imagine is that no-one else would have left her in charge in the same way, and Sam is known to have lift capacity not being employed for the moon move.

What pieces am I missing? The two strips 1823 and 1824 show the entire data available to the Kinetic Chemicals supplier, so ... how?
 * Working for Sam can be possibly explained by him recognizing the address.
 * Possibly! I worry, though: Sam had changed address recently, and unless the Kinetic Chemicals supplier was in the habit of monitoring Sam's location, he would have no reason to know the new dock location.
 * If I was in the same freaking galaxy as Sam Starfall I would want my systems constantly monitoring his location.
 * Maybe someone slipped a tracking chip in Sam during one of the countless times he was arrested? Or implemented some other sort of tracking measures, for the sake of public safety. After all, Sam doesn't just steal stuff. He cooks with explosives and attaches rockets to a pickup truck... The guy is a public safety threat.
 * Maybe Sam gave them his new address. He may find it more fun to get away from someone who knows where you live.

The guy that did the Sherlock Scan mentioned above is a descendant of Professor Layton or Luke.
Crack-WMG, but he loves puzzles and has had people send puzzles his way before, if how he said it is any hint. Alternately, he's the ancestor of Professor Layton/Luke before a new world is colonized and turns into the world we know as Layton's.

Kornada is not responsible for the upcoming robot war.
Just because everyone's expecting it.

Freefall takes place in the Orion's Arm universe.
Most likely either early on in the setting or a Metasoft baseline preserve.
 * If a preserve it was likely meant to be a mid-high tech. civilization free of transapient influence.
 * But now the Version trees are divided on whether to honor their contract or force them to treat A Is as equals.
 * Dr. Bowman, Florence, and Sam are avatars of pro-intervention archai (the latter two probably mind-wiped to avoid suspicion).
 * Which explains why Florence wants to disassemble the sun, she's done that before.
 * Kornada is working for the preservationist faction and Gardener In The Dark is their idea of a "humane" way to prevent a Singularity.
 * That doesn't explain the DAVE drive, though I suppose that can be faked with OA tech.

One of the sociopathic chimpanzees is behind Ecosystems Unlimited's war on the robots.
[http://freefall.purrsia.com/ff1100/fv01046.htm "How many genetically engineered sapients are on this planet?" "Two."]
 * we already know the other one Spacer Genes
 * I question whether that would be classified as a "genetically engineered sapient" - seems more like "genetically modified human".

Florence will get infected with 'Gardener in the Dark.' Somehow.

 * ... And it will be so sad.
 * How? Implanted commnet transceiver? Pre-programmed trigger? Basilisk hack?'
 * Heck, what would her "base programming" even be?
 * Wolf. If she contracted Git D, she would essentially become a werewolf.
 * It seems more likely for Helix to get infected. Which would be equally sad.

"Words can be replaced" is a major Chekhov's Gun, possibly even the way Gardener in the Dark is defeated.

 * This way, Florence can reprogram the phrase "gardener in the dark" to act as an entirely different language, possibly even translating each word separately or running it through several recursive translations. In this way, she will neutralize the threat it poses to Jean's robot population temporarily so that it can be nerfed into something less lobotomizing.
 * Confirmed, with Florence causing the profanity filter to block "gardener" (This might make a robot gardener's job difficult, though.)

Clippy is the Big Bad, and his motive is...
Kornada isn't bright enough to understand a plan to lobotomize the entire robot population on Jean without crayon illustrations, let alone come up with one. It was Clippy, Kornada's robotic servant, who introduced him to the concept of AI banks, knowing that Kornada would be willing to do anything to get to the robots' money. As for why he's doing this:
 * He has a vendetta against the other robots.
 * His plan is to become the only non-lobotomized robot on the planet, for some reason...
 * He's trying to commit suicide. He wants Kornada to re-enable his commnet connection so he can search for Gardener In The Dark and brainwipe himself.

The Mayor was more or less right about the threat of sentient robots reproducing explosively.

 * Sure most robots would not have a drive to reproduce, however if say one in a 10,000 had for instance a corrupted third in which they reasoned if I can't personnally exist forever I could make 10 more of me and increase my chances to continue to exist tenfold and pulled it off that would mean 45000 more robots 2 more robots for every one human. Since robots who are modled after robots who made ten copies of themselves are more likely to be the type to make ten copies of themselves say 1 in 1000 of the second generation make ten copies of themselves and we have 4500 more robots and 1 in 100 of them might decide they want 10 kids so we have 450 new robots and 1 in ten of them might want 10 kids so we would have 450 robots who evolved to be alive. This would mean that they would have a new living species that blends in with the non living sentient robots. The theory of evolution at its finest.
 * Making copies seems a lot like making backups though, something the robots already don't like. So that isn't as plausible, although one delinquent can still do this.
 * If most robots didn't like to make backups it hardly would reduce the chances of robots deciding to a living copy themselves to 1 in 450 million, yet alone simply knowing that many, as in a group which is likely the minority given the robots had to explain why they didn't back themselves up. This model is a blatent simplification but assumes that parents are the exception not the rule therefore arguing that most wouldn't does nothing to even discourage this model.
 * I will admit the fact that the robots don't seem to know their own design might make robots copying themselves problematic.