V-2009/WMG

The Vs came to Earth because of the Combine.
The reason they come to Earth is because the Combine invaded their home planet. They did to it what was planned for HL2 (I.E. they changed the planet's atmosphere to be more Combine-friendly), and this screwed over their ability to reproduce. So the few that managed to escape the Combine end up making their way to Earth on a ship they had from before their version of the 7-Hours war (which, given the rough tech level, probably lasted more along the lines of seven days - in other words, enough time to evac the then-queen - Diana - and a moderate amount of V's trained for multiple tasks.)

The reason why Anna's adopted the hatred for Human Emotion is because the Combine did some experimenting. The V's originally did have emotions. But the Combine, with their ability to bioengineer things (such as Striders and Gunships), released some sort of agent that caused V's to see emotion as useless - just like one would figure for an Overwatch soldier or a Hunter. The ability to hatch V's that fill different roles is natural - the Combine had nothing to do with that (though it is possible that they DID inspire some technologies.)

The Combine have not yet decided to come take the V's back. They see no point in it - yet.

End of the show
The show will end with Anna and Diana killing each other in all-out duel, and Lisa becoming a new Queen. She will convince other V's that Anna enslaved them using Bliss and will replace it by teaching V's human emotions. Lisa will also forge a true alliance between V's and mankind. At some point Marcus will turn against Anna, being convinced she can't handle emotions. He may even join Fifth Column (temporary) and in the end will be killed either by good guys or by Anna.
 * Somewhat Jossed, as
 * It's possible Marcus may join the Fifth Column,.
 * There maybe a duel between Anna and Erica,.

V is for Vasari
The V ships look rather similar to Jarrasul Evacuators. And we've never gotten a good enough glimpse of the V's to discount them being Vasari.

V is for Vendetta
The Vs have come to seek vengeance on humanity for what our long-forgotten Ancient Astronaut ancestors did to them when they were in a primitive state.

The Vs are Artificial
The Vs were genetically engineered by Neglectful Precursors from Earth life. This explains how the V's biology is compatible with their human 'suits', how they can seemingly digest human food, and. Also, Anna mentions to Lisa that they where "designed" to be efficient, implying that they where created for a purpose rather than evolving naturally. They need Earth in particular, rather than the bazillions of other planets in the galaxy, because as their original homeworld it is uniquely suited to their physiology.

John May is Erica's ex-husband and Tyler's father.
While he was apparently the leader of the 5th Column for a while, John May disappeared for some reason. Perhaps it was a similar situation to the one Ryan faced, where John fell in love with a human--Erica--and decided to leave the Resistance rather than put her in danger. They had a son, and somehow (admittedly, this is the biggest flaw in the theory) concealed Tyler's status as half-human, half-V from both him and Erica. Then, when he learned Anna and the V motherships were about to arrive, he decided that simply laying low wasn't enough to keep his family safe and decided to disappear completely. Unfortunately, Anna somehow became aware of John May's family, and that is why she's so interested in Tyler: because he's the only half-breed they know of, and because he could potentially help the Vs to find John May.
 * Have my babies. Please?
 * /Elizabeth Mitchell would be interesting.
 * Possibly Jossed as of episode six, but it's still too early to tell.
 * Almost certainly Jossed as of episode 7.

Tyler is a half-human, half-visitor hybrid.
This is the big secret about him, and Erica and Joe have always known about it. In addition to this, Joe must also either be a V or he isn't actually Tyler's real father (going on the theory above that John May is). It's hard to tell if Anna knows of this or not, but given how special he seems to be to Lisa's 'destiny', it seems probable. It's also possible that Erica may not be his real mother either.
 * The tidbit of Joe not being Tyler's father.
 * Jossed: we see a half-V hybrid and Tyler is special for other reasons:

Erica is part or full V, and Valerie will also become one.
Going by what Joshua said to Ryan that there'd be 'no going back' once he gives Valerie the phosphorus, and that a human cannot survive the pregnancy, this seems to be the likely outcome. If Tyler is in fact a hybrid, then the same thing must have been done to Erica as well (if she is his mother), and she has always known about it.
 * Appears to be Jossed now, especially since.
 * Jossed:

Anna is an Eldritch Abomination, and not really a V.
Except for (maybe) her daughter, she truly doesn't care about anything or anyone but herself and is using both the Vs and humanity for some truly evil purpose. At some point in the past, she took the form of a V (and killed the real Anna, if there was one) and enslaved the entire race. Her ultimate goal is either to rule / destroy the universe (of course), or release some horrible Sealed Evil in a Can that is her master and much, much worse than her.
 * If this is true, then this evil will destroy Anna since she outlived her usefulness.

Joe really is Tyler's father, and a V doctored the results.
Maybe he is somehow biologically compatible to father a hybrid, and everything since then has been a huge Xanatos Roulette on the part of Anna to eventually get him to mate with Lisa to produce The Chosen One, or something of that sort (since Anna refers to her daughter as being ready to fulfill her destiny). Though why they couldn't just force him or steal his sperm isn't made clear, unless hybrids can only be produced by The Power of Love. Too bad they didn't count on the possibility of a male V impregnating a human woman, though there's no telling if the hybrid in that case would be anywhere near the same.
 * Semi-confirmed:.
 * Joe knew of this, he was an unwitting pawn. That's why he and Erica got divorced. After many years, he didn't want to hurt Tyler anymore. The bike accident may have been the incident which led him to that decision after all, just not the sole reason as Tyler always believed.
 * Jossed as of the fifth episode of Season Two; Joe had no idea.

John May is Jesus, and he rose from the dead after three days.
Because Fifth Columnists keep posting the message "JOHN MAY LIVES!", and who would risk their lives to spread a message that wasn't literally true?
 * To spite Anna. Also, it's not exactly clear how many Fifth Column members know Presumably the ones who were part of the original resistance do, but it is perfectly clear that there are a lot of people who only recently joined the Fifth Column. But mostly, to spite Anna, as is explicitly stated by Ryan at one point.

Anna is Diana from the original.
After the events of the original series, everyone returns to normal life. Many years later, Diana leads the Visitors back to Earth, now with improved voice synthesizers and immunity to the colour red. For some reason, the inhabitants of Earth do not recall the original Visitors, and welcome the new "Vs" with open arms. Alternately, every member of the human race with a decent recollection of the original invasion has already been replaced by a Visitor.
 * Jossed:

The Visitors do not (or can not) clone human skin and other tissues.
Instead, they simply abducted and killed people and harvested their skin, and then somehow designed human forms from it (mixing and matching to avoid being recognized as someone who went missing). In the case of infiltrators, it is likely in some cases that they probably killed the real person who existed and then assumed their appearance and identity.
 * Jossed:

Anna is not really in command.
She only thinks that she is, but Marcus is really the one pulling all of the strings and eventually plans to completely overthrow her (and by extension, Lisa). Given that he's involved in dealings with people seemingly without Anna's knowledge, this may be possible.
 * Alternate theory: Anna is the ambassador and commander of the Earth-conquering fleet. She has superiors on her homeplanet who begin to question her following the "red sky" incident. Marcus is either The Starscream and/or the Dragon with an Agenda.

The whole Red Sky deal is meant to make humanity utterly dependent on the Vs.
Even though she jumped the gun, Anna's original plan of making humanity dependent on blue energy seems to indicate that she wants V tech to be running basic services. Now that yellow sunlight is blocked out, humans will have to turn to the Vs for either bioengineering or some other method of manufacturing breathable air since all the plants are going to die.
 * Jossed: Red Rain supposedly repairs the ecological damage humans have caused,.

The whole Red Sky deal is meant to stop Superman.
We all know Superman gets his powers from yellow sunlight, so the plan is only natural. This version of Superman isn't as public with his gifts, so people don't really know he exists (sort of like Clark in the early seasons of Smallville). But the Vs found out, and they know he'll bring the pain if he figures out they're not on the level.
 * Jossed.

The series serves as the direct prequel to End War.
In the aftermath of the Vs' defeat, the Russians figure out how to copy Blue Energy (hence the US raid on a reactor).

Erica's going to get a lot more manipulative.
And I mean a lot more manipulative. Probably not on par with Anna, though. Erica's definitely planning to in one episode, where she says that since Anna is using Tyler against them, she's going to use Lisa against Anna. Erica does manipulate Lisa in that episode, and might have succeeded if Anna wasn't in the room. Since then, she's had a noticeable tendency to manipulate others. Not to mention how most of the characters are getting darker.
 * This is especially likely since it sounds like Erica plans to continue having regular dinners with Anna, Lisa, and Tyler. In doing so, she's going to have to manipulate both her son and Anna at least into thinking she's pro-V, and will probably go beyond that.
 * That scene at the end of the premiere for Season 2? It means that Diana is the Bigger Bad.
 * Nope, Anna locked her in the belly of the mothership in a coup. She's actually just about as close to a Big Good as the Vs can get, as she's the only one who understands the concept of the soul.

Another race will come to kick V's asses.
Because it would be awesome to see. Now, when we see that their goal is to make many half-human hybrids, maybe they are making an army?
 * Related theory: Survivors of other races who's planets were conquered by the V's joined together as a rebel alliance. Their goal is to defeat the V's and save the galaxy from being enslaved/eradicated.

Marcus is a deep-cover Fifth Columnist.
Due to his position as Number Two, nobody in the Fifth Column knows it (he'd have to meet with others heavily disguised and under a pseudonym). It is not a coincidence that every single one of Joshua's memories concerning the Fifth Column are gone. Marcus wiped them out to protect everyone, and may or may not have viewed them beforehand. Remember that at the end of the first season, Joshua wakes up briefly and still seems to (for the moment) retain what just happened, and Marcus was the first person to see him.
 * As of late Season 2, especially the finale, this is just not possible. He wouldn't have put himself in harms way to save his Queen if he was working against her.

Betrayal is a twisted tradition in Anna's family.
As revealed by Diana, Anna betrayed her and took command. Diana said its only a matter of time before Lisa will too. Diana may have betrayed her own mother, who betrayed her mother, and so on. However, Anna was rather angry at Diana for suggesting that Lisa would betray her. Either she's in denial or she believes there's no reason for Lisa to betray her since they were much closer than she was with Diana. Her emotions must be the reason. Since Anna injured her own daughter to gain sympathy, this may lead to Lisa betraying her own mother. But only for a different reason, Anna wanted power, while Lisa wants to save Earth from her own people.

Anna will suffer a really big Villainous Breakdown.
Her failure to destroy the human soul, her daughter's betrayal, Marcus's treachery, and her rising emotions will all be contributing factors.
 * not big enough for you?
 * That's only the beginning.

Diana is the Bigger Bad
As of the latest episode, Lisa hugs her and tells her that she's the only one who understands what she's going through. Lisa then gives Diana something that will allow them to stay in touch. As Lisa leaves, Diana smirks evilly. I guess emotions have made her stronger, and all the more manipulative.
 * Unless she plans to use it to escape.

Marcus is Lisa's father, as well as father of the queen egg.
As implied in the Sex scene with Anna in order to have certain "breeds" of V's, the Queen, or perhaps any V female, has to mate with the male of that breed such as the soldier that Anna mated with. This would imply that Marcus is "royalty", or at least as close as you can get to royalty for a V, himself. This may explain why Marcus is able to advise her and even questions her orders sometimes with no repercussions. It may, also, explain the rage that Anna felt over the fact that Marcus was nearly killed. Of course, this doesn't explain why Anna didn't.
 * This could also be part of the reason that

Project Ares is X-COM under a different name.
Search your heart you know it to be true.

V takes places in The X-Files Universe
And is set between the end of the TV show and the second movie. Joe Evans is actually Krycek who sold his wife and son out to the Vs (because that's what he does). This also explains why the FBI take the existence of aliens totally in their stride. Mulder would, of course, save the day if he wasn't too busy growing his epic beard out in the middle of nowhere. The show finale (in 2012, if the Cigarette Smoking Man is to be believed) will be a war between the Vs and the Grays, which will destroy both sides leaving the remnants of humanity to rebuild After the End.