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The Captain is female.
Word of God says that one of the characters is female and so far, all the evidence seems to point to the Captain. S/he's referred to as a "little girl" on more than one occasion and the jumpsuit-thingy girl the comic's creator draws might be the same as the girl on the operating table featured in the Captain's song. This is either confirmed, or the author is messing with us; many of the pics of the Captain that the creator has posted to Deviant ART are in the "females" category: .
Romantically Apocalyptic is set in the same universe as Gone With the Blastwave.
The Captain and the rest were simply cut off from their respective armies at around the same time the bombs fell, and thus had joined up for the purpose of survival (due to the lack of friendly soldiers and thus supplies) and friendship (due to boredom). Their uniforms are old pre-war clothing and masks, which explains why they don't look like their original armies.
The Captain is a Hermaphrodite.
While there is evidence to suggest that the Captain is a female, perhaps s/he is both male and female at the same time: The "Que Sera" video states that his/her DNA and Chromosomes were altered when he/she was little. Thus, if the girl/woman in that video is indeed the Captain, then perhaps s/he started life as a female, but took on male characteristics due to this tampering, such as a deeper, male-like voice, superior strength and endurance, etc. Therefore, s/he is both male and female at the same time. Also, the Captain is found to be horridly radioactive. There's no way that his/her biology isn't affected in one way or another. Furthermore, this image, submitted by a fan for a contest, was posted to the author of Romantically Apocalyptic's Deviant ART account, categorized as "Customization/Wallpaper/People/Males." However, as of this posting, the author has changed the category to "Customization/Wallpaper/People/Females." Either this is evidence for this WMG, or the author is messing with us by changing the gender every so often (or both). To top it all off, the Captain is modelled by both men and women.
Alternately, the Captain is MtF.
No transition or anything because there's no way she could get it, but may explain the deep voice despite other contradictions. The girl/woman in the video is indeed the Captain, but it's more how she sees herself than how she really was. In one of his journals, Pilot refers to the Captain, saying "EVEN THOUGH I WASN'T BORN A 'LITTLE GIRL IN A STRANGE AND FORGOTTEN COUNTRY FORMERLY KNOWN AS GERMANY'..." The fact that he specifies "born a little girl" seems to suggest that this was a temporary state.
The Captain is male.
Since Snippy and Engineer are confirmed to be male as well, this would presumably make Pilot female.
The Captain's real name is Zee Captain
Well, Mr. Snippy's last name really is Snippy, so why not? And it is a bit strange for someone who speaks fluent English to refer to themselves as "Zee Captain" instead of "The Captain." This strip might lend credence to this, as in the description, Engineer refers to him as "Zee Captain" despite his serious personality and the otherwise grave tone of his entry.
That chick on the billboard at the beginning is the female character.
Either that or it's between Pilot and Zee Captain. In the journals written on the author's deviantART, the entries written by Snippy use "he" for Pilot but avoid assigning any gender-specific pronouns to the Captain (again, it's possible that this is a case of Unreliable Narrator).
Something terrible will happen if the Captain's gender is mentioned.
Because (as mentioned above) In-Universe, Snippy specifically avoids referring to the Captain as "he" or "she" in the journals. This would make sense if Snippy honestly didn't know what the Captain's gender is, but, as explained in this  journal, Snippy knew the Captain when he/she was "Subject Seven" and mentions having seen footage of him/her causing trouble involving tea being spilled on electronics. There wouldn't be any reason for the Captain to be wearing a gas mask before the apocalypse, so Snippy should have seen the Captain's face at some point. It's much easier to use pronouns like "him" or "her" when talking about someone else (as Snippy does when mentioning Pilot), but for some reason he refuses to label the Captain as male or female. So, either the Captain's face and voice were so androgynous that Snippy couldn't tell his/her gender, or Snippy can't tell anyone about the Captain's gender. It's also possible that the Captain always wore a gas mask even before the apocalypse, because s/he's just weird like that.
Sniper is The One Guy.
And everyone else is a girl.
- Jossed: Engineer is male as well.
The Captain accidentally caused the apocalypse.
The real reason Snippy follows him/her around is to make sure s/he doesn't mess things up further (after all, the fact that there are still living creatures -- even if most of them are freaky mutant things -- implies that there may still be some hope for the world). This seems to be confirmed by a comic revealing that "he spilled tea on the server banks", and Engineer's outburst at Captain, proclaiming, "This is all your fault!" This is also mentioned on Snippy's Tumblr, when a fan asks who he blames for the apocalypse. Then there's the fact that in an early comic, Captain is finishing a "conversation" with a skeleton with, "...and that's how I caused World War 3." More specifically, Captain's tea destroyed several server banks, and, feeling threatened, ANNET killed everyone in the facility and took over everyone who was connected to the neural network. In order to shut her down, Engineer had to nuke the place.
The Captain intentionally caused the apocalypse.
Because s/he thought it would be funny.
Snippy has a thing for Captain.
If the Captain is female, (or even if he isn't) then if you think about it Snippy being Tsundere for Captain totally makes sense. Note how he chooses Captain as his favorite... friend, and his reaction when he finds out Pilot's taken Captain from him.
Snippy is immune to Cancer.
In the flashback/illusion episodes, he was unable to use the mental network. So he is most likely the new saviour of Earth.
Zee Captain is Haruhi Suzumiya.
And Snippy is Kyon.
Zee Captain is a Time Lord.
And that mug he always carries is his TARDIS.
And the Cancer is Satan.
Captain and Sniper are reincarnations of Krazy Kat and Ignatz.
Snippy's status as The Chew Toy is Ignatz's karmic punishment for being so cruel to Krazy. This would also explain the confusion about the Captain's gender -- George Herriman (the creator of the Krazy Kat comic) described Krazy as "androgynous, but willing to be either" and there's no reason why this couldn't also apply to his/her reincarnation.
Although the authorship of The Ugly Barnacle is generally attributed to Mr. Patrick Star, its origin is shrouded in mystery. It's possible that someone else (most likely the Captain) wrote it as a document of how the apocalypse occurred. If so, then the eponymous protagonist is probably ANNET, who is portrayed as a barnacle for the sake of symbolism.
Zee Captain is destroying the universe.
Albeit, probably unintentionally. In strip 27, the Captain complains that the universe is shrinking. This may seem like nothing but a simple fourth wall joke/Captain being crazy, but in strip 28 the screen-faced alien says the Captain's theory has apparently been confirmed by the 'universe science compendium' and the universe is shrinking at an exponential rate. And that this means everyone in the universe is going to be crushed into nothingness. Later on in strip 51 Cancer refers to Captain as a singularity, and in the comments of a later strip as a 'temporal singularity'. Singularitys, theorized to be found in the innermost parts of black holes, suck things in. Therefore, the Captain is a singularity, drawing in the universe itself at an exponential rate, and slowly dooming the entire universe. Since the Captain expresses displeasure at the thought of the universe shrinking in strip 27, I assume that the Captain isn't doing it deliberately or even aware that they're the cause.