Allen The Alien knew Nolan was a Viltrumite from the beginning.Allen The Alien has spent all his life working to oppose the Viltrumites, whom he hates passionately. He then comes upon Earth, where the people all look more like Viltrumites than does any other species we've seen. he then fights one of them, who displays Viltrumite-level abilities, and has a mustache. Clearly, he must have known right off the bat that "Omni-Man" was a Viltrumite, and might have even assumed that Earth was a massive Viltrumite colony. Since Omni-Man let him go alive, he kept coming back every few years, to try and determine the Viltrumite's mission. When he fought Mark, a possible non-Viltrumite with great physical powers, his superiors ordered him to inform the other hero of the situation, so the two could ambush and kill the Viltrumite together.
The Viltrumites could never truly conquer Earth anywayJust the number of superpowered characters in the series proper itself is staggering, and then when you combine that with the fact that it's also part of the larger Image universe who have some massive heavy hitters living there as well the deck is already stacked against them. They've already driven off much larger invasion forces (from a species that even gave Omni-Man trouble) and now we have two Viltrumite hybrids on out side as well a Allen (who is quickly surpassing Viltrumite levels of strength). Furthermore the way that Omni-Man disposes of the original Guardians suggests that he knew that he couldn't win in a fair fight against all of them. Earth would finally be the death of the empire.
The Immortal is a Ti- Argh!Sadly, the author of this theory appears to have vanished before finishing it. We may never know what it was meant to say.
The Immortal was Abraham Lincoln.In his Origin, he talks about leading the people of the Americas, while a shot from behind shows a man in a stovepipe hat, speaking before a large crowd. Perhaps a younger, more patient Immortal was once the nation's most famous president - it would help to explain the unique deference Cecil shows him.
Darkwing is still alive.Hey, we don't have the body. The Invinci-clone Darkwing pulled into the shadow reality was not as wise as core Invincible, and let go of him. Unfortunately, before Darkwing could come back out, one of the creatures there grabbed him - once he fights his way free, he will return, even more dangerous.
The Great Thaedus is still working for the Viltrumites.He founded the Coalition of Planets to gather all the resistance to their rule in one place. When the time is right, he intends to crush it in one fell swoop. He is the leak who told the Empire about Nolan's betrayal, and by taking orders only from him, Allen is playing right into his hands.
Mister Liu cannot retain spirit form very long.When trying to cross the ocean, he stayed airborne for too long, and fell, causing himself and his minions to drown. This is why they never showed up for revenge on Titan.
Kursk is secretly behind everything.We know that he's rather intelligent, but has trouble communicating with people who don't speak Russian. What we don't ket know is that he uses this intelligence, combined with near-limitless powers, to manipulate the entire population of the Earth, and beyond.
Mister Liu is Master Li.The names are similar and Liu certainly has the power and underworld influence one would expect the Glorious Strategist to aquire, but the clincher is that his spirit form is a giant dragon. Clearly, he got this form by absorbing the godly powers of the Water Dragon centuries ago. His mortal body could not contain all that power, thus the need to project it externally.
The Order is a group of cyborgs who united to Destroy All Humans!.The only members we see are Machine Head (self-explanatory), Mister Liu (robotic lower jaw), and Titian... who gained his position through violent treachery, and was rejected by the rest of the Order. With his stone form, the Order was not sure at first he was simply an inferior human - when they found out, they declared war on his operation (concern for the loose cannon Multi-Paul was just an excuse).
Rex Splode was created by the program that made Atom Eve.His "secret origin" mentions that he was created by the government to be a weapon, and that's what the Atom Eve project was. Plus, his power can be interpreted as a form of matter transformation (just into energy, not other matter).
Controlling robots larger than a certain size is dangerous to Robot's mind.This would explain why he never uses the bigger (seemingly more powerful) drone he used to defeat the Mauler Twins again.
The wife that Omni-Man misses is Oliver's mother, not Debbie.He only ever mentioned missing his wife after leaving her, and it was her planet, not Earth, that he stayed with to protect from the Viltrumites.
Anissa will try to seduce Mark.After the end of the Viltrumite War, the stated goal of the Viltrumites on Earth is to breed with humans. However, Anissa, being a proud warrior race woman, is clearly shown not to be impressed by weak human guys. But Mark, the guy who defeated the second-toughest Viltrumite of them all, might certainly be an acceptable mate for her. So Anissa will try to get Mark sire a kid for her, which of course doesn't sit well with Eve... Some Unwanted Harem action will ensue. It's also likely that Anissa will later on undergo a Heel-Face Turn, first of all because it's more likely to happen to an attractive female villain, and secondly because she is the only one of the villainous Viltrumites who hasn't been depicted as a murderous sociopath.