The War of the Worlds/WMG

The aliens are really super-modified humans from the future.
They found some of The Time Traveler's work (or independently discovered the secret), and when future-Earth's resources started becoming depleted, they realized that a relatively easy solution would be to colonize a past version of their own planet. (Cavorite doesn't help with crossing interstellar distances.) Pretty standard twist, but it helps explain why Earth diseases killed them.
 * Note that this theory meshes well with H.G. Wells's ideas. The design of the aliens is explicitly based on Wells' earlier work "Man of the Year Million", in which he posits that, eventually, mankind will evolve away from the need for conventional bodies and will simply be brains and tentacles, completely dependent on machines.
 * Of course, the idea that Mars is a slightly older planet than Earth with more "highly evolved" inhabitants (brains with tentacles dependent on machines) is fully consistent with the 19th-century theory of planet formation.
 * Presumably, the future-human "Martians" come from a time after the common cold has been cured -- so far after that they've forgotten entirely about its existence and how to create the cure (or a decent antibody).
 * Alternatively, it was a different disease that took them down. The protagonist supposes it was the common cold, but it could as easily been the flu or even the one of the symbiotic bacteria that everyone has, but which had changed so much by the invaders' time that they were incompatible with the modern version and were killed by it.
 * possibly so called 'Friendly' bacteria....Death by Yakult!
 * If memory serves, it's explicitly chicken pox in the Recycled: the Series.
 * Chicken Pox, schmicken pox. Nothing can outmatch Latobacilli, SHIROTA STRAIN!!!!!! 
 * Maybe it wasn't that the bacteria or viruses infected the Martians per se. Maybe bacteria got to places that didn't take kindly to having a layer of bacteria covering it, and the Martians died just as a person would die if their internal organs suddenly got coated in a foreign substance.
 * Death by PeptoBismol?
 * Wasn't this the premise of The Time Machine? Not like Wells to repeat himself like that.

The Martians were afraid of us and acted out of paranoia.
Human technology pales in comparison to Martian tripods, but our computer processing power doubles every eighteen months and soon will double every other month. They saw we were advancing very fast and, in a panic, built war machines to wipe us out. It would explain their Cool but Inefficient way of wiping us out (using dozens of huge machines instead of, say, some sort of nuke) and their fascination with a bicycle wheel in Spielberg's 2005 version. They skipped the wheel in their history of technological advancement, which is why all their machines walk on legs and move so organically.
 * If that is true, the Martians must also be idiots, since an orbital meteor bombardment would be far cheaper and more effective at the whole wiping-out business.
 * In the original version, Martian space travel was too primitive to allow them to steer asteroids- they were limited to payloads about the size of what a Saturn V or its immediate (hypothetical) successors could throw, and they didn't manage to launch very many.
 * As to why they didn't use nukes, again, because the author didn't think of them (yet). The weapons used by the Martians were quite reasonable as advances on technology that already existed at the time: poison gas (used in World War One), and giant mechanical war machines (used in World War One and later), and the heat-ray (while historically it's taken us a hundred years to advance our ability to manipulate electrical energy to make beam weapons, it was not unreasonable for Wells to assume that advances in radio and electronics would make things faster than that).
 * Humans didn't have computers back then, so if they were afraid of our technology, they must have based it on something else.
 * Our computer processing was doubling every eighteen months. Try a doubling series sometime. It would be about forty-five years between this story and UNIVAC. There was two billionths of a computer's worth of processing power back then - hardly enough to notice, but it quickly became a threat....
 * How would the Martians know we were going to invent computers that would double in power unless they already had computers? In which case they'd be ahead of us in the doubling cycle and have no reason to fear us.
 * Martian technology is advanced Steampunk, as befits the fact that it's a story dating to the end of the Victorian era. By modern standards, Wells's Martians didn't have computers, though they might well have electromechanical analog computers of the sort humans used during WWII. They're not afraid of computers, though; computers simply do not exist in Wells's setting.
 * Wells lays out a perfectly good reason for the Martians to attack Earth in the original: Mars is dying and they want to colonize Earth. That stopped making sense once we realized Mars is already barren, which is a problem for the 2005 edition, I guess.
 * The 2005 version doesn't explicitly say they're from Mars.
 * They were obviously scared of our wheels. Bicycles and horseless carriages had nearly the effect on them as seeing Alien Geometries would have on us. They sent their strongest minds to face this threat head on, but in their panic did so without proper preparations.
 * Um... how could they NOT have invented the wheel? The wheel is, like, the easiest thing to make in the universe. They invent Humongous Mecha and Death Rays and god knows what else, but they never considered a little round thing with a hole in the middle? No wonder they died of bacteria.
 * The Martians not using wheels was an early subversion of Technology Levels. The idea of a technology that developing early in one place not coming along until much later somewhere else has precedents. In hindsight, it always looks obvious.
 * If the Martians were amphibious (which makes sense, judging from their octopus-like appearance), then they might not have invented the wheel. Wheels don't work that well underwater. Instead, they might have made the tripods much later on to help them move on land.

Whatever powered the Tripod's forcefields had to be constantly kept in check.
Perhaps it was powered manually or by the aliens brain power, which is why the shields began to fail after the aliens got sick? The aliens may have had to crank operate the force fields, or fuel it with some kind of substance, or even willed the force fields to exist themselves.

The Martains are the precursors to the Anti-Spirals
A continuation of the theory above: it was the rapid growth of humanity that caused them to fear other spiral races (such as humans) in the first place.

The Martians weren't fighting us; they were running tests on our planet.
Just look what we're doing on Mars: running local substances through combustion chambers to determine chemical makeup. Picking up interesting rocks. Landing on things with no regard to what might have just been flattened. Sound familiar? The "Martians" weren't even the real local species: they were artificial constructs created to test if there was anything fatal to the real Martians. (There was. They'll send another wave once they figure out how to stop the disease.) They sent Terran Land Rovers.
 * But then how to explain their use of massive clouds of poison gas and Heat Rays on any humans that got close? We don't equip our Mars probes with machine guns and start shooting up the landscape at random, after all.
 * Those were not weapons, they were a test of chemical reactivity, and laser spectroanalysis.
 * They used heat-rays as weapons against attacking forces on a regular basis, and went far out of their way to spray poison gas on populated areas (like London), even after they would have to know the lethal effect those devices had on the natives. At best their research equipment was being used with homicidal indifference to its effects on the local population, by Martian operators who were physically sitting in the machines at the time.
 * As Wells put it, they were "intellects cool, vast, and unsympathetic."

The martians were the "zeroth" angels.
Just messing with ya. If you want to make a "serious" Evangelion theory, I'd love to hear it.

== The angels attacked because they thought   was the amazing technology that killed off the martians without leaving a mark or giving them time to escape. == The different angels wanted to either kill the humans to prevent another genocide, stop the humans from being killed, or take the weapon for themselves. The Martians were not really killed by a human disease, but rather  interfering with the martians' weak fields and turning them into, not Tang, but Jell-o. If  visited Earth, we'd be the dead ones.

The Tripods were EVA units
This may only work for the remakes, but I'll go with it.

The only visible difference between the aliens and their Tripods is one of height. However, something about the way the tripods move is just too organic (and some parts of them look downright fleshy).

The shields that turn up in every remake are not force fields, but AT Fields. The AT Fields falter because the Tripods themselves are sick. Hence why, at the end, they weren't able to do much but fart at people, and why Tom Cruise was able to kill one-he was already inside the field and could damage the core.

Even more evidence-when the soldiers opened the hatch that lead to what was probably the cockpit, a shit-ton of orange fluid spilled out, followed by the dying pilot. What other mech works this way?

The future Earth of WOTW is Code Geass
After the end of the original novel it was most likely that decades after the failed invasion of Earth the Martian species did become extinct. Also the end of the Novel also details how humans were deeply researching the martians highly advanced tech and physiology so it could be assumed that at some point Great Britain began to secretly reverse engineer the Martian tech to create their own Humongous Mecha.

And since Britain was still in their Full swing imperialistic Bastards period they most likely forgot that they weren't the most powerful nation on earth (or in the universe) anymore and used this reengineered tech (ie, Steampunk prototype Nightmare Frames) to start colonizing other lesser advanced countries en masse. At some point afterward the Royal House of Windsor was overthrown in a military coup led and or funded by a family of nobles calling themselves Britannia.

After that, things go downhill for the rest of the world from there: more countries are annexed by Great Britain and are included in their now vastly growing "Britannian Empire" and probably around sometime in the mid 20th Century since they had taken over so much new property Britain began to designate various countries/land sectors as numerical "Areas" to easily keep track of all they owned. However this led to extreme forms of racism and discrimination by the British public now referring to the native population as their countries respective numerical designations not by the nation they originally came from.

Japan was Probably taken over and Annexed at some point in either the 1960s or 1970s and designated as Area 11. As for Geass itself it might be a form of reverse engineered Martian genetics as Wells himself wrote that the Martians probably did use some from of telepathy to communicate with each other.

If anyone else has anymore theories on this please feel free to add...

The Martians were genetically engineered lifeforms.
Their physiology is extremely efficient & deliberate, which is not generally something that happens with natural selection. This may also be the reason they died out. Because each of them was optimized to the same standards it resulted in a lack of genetic diversity, making them more vulnerable to disease. Once something figured out how to infect one, it could kill every single one of them.
 * A lack of genetic diversity is only a problem in the sense that it leaves a species unable to evolve immunity to a new disease. But the Martians all died at the same time, within one generation. They had no time to evolve anyway. All the genetic variability in the world(s) couldn't have saved them.
 * The most likely candidate for who engineered the Martians? The Martians themselves. Seriously, they're Wells's idea of what a super-advanced race of intelligent beings will tend to make themselves into, and this was before the Nazis turned any support for eugenics into major Values Dissonance. The Martians probably modified their own bodies to increase their intelligence and tool-using ability at the expense of making them more reliant on support machinery, some time in their own past.

The Martians not only genetically altered, but are actually artificial lives who Turned Against Their Masters.
A brief mention is made of another race of vaguely humanoid Martians that the invaders used for food before they started sucking human blood. These are actually the things that created them. The invaders were created as a race of biological computers who tired of their servile role & took over, but the resulting war of independence rendered Mars uninhabitable. Their cruelty to humans is partly because they remind them of their former masters, both in appearance & the way they treat their own "lesser" races.

The Martians of War of the Worlds are the same as the aliens in Metal Slug
After losing an attempted invasion which resulted in high Martian casualties the remaining Martians stayed on Mars and began to repopulate. After around 100 years they noticed that the world was already involved in a giant war and so decided to invade on an unexpected, unprepared and already damaged world.
 * Also, if you remember how the book describes the martians and then compare them to the Metal Slug martians, both appearances are similar. Must have been a Homage.

The 1938 broadcast was real.
Orson Welles was trying to root out the real aliens, but they got to him and foced him to change his story.

The Tripods in the movie were Lost Technology created by The Galactic Confederacy.
It certainly fits, considering how long they've been buried and the fact Tom Cruise is there.

The Martians had a colonialist society, or at least one with little equality, back home, too.
Those skinny, vaguely humanoid things they brought with them as rations are actually the species they were bioengineered from, though perhaps a different ethnic group. Only the rich had the money to improve themselves with biotechnology, and once they had "evolved" themselves into a totally different species, they no longer felt there was any reason to treat "lesser" peoples as anything other than resources to be used and discarded.

The Heat Rays in the Spielberg movie were actually energy-leaching beams
As mentioned in the article for The Film Version, the rays vaporized the people, but left their clothes intact, floating around in a really ridiculous way. This troper believes that those beams were really some sort of beam that sucked out all of the energy or water-content (dehydrating the victims) of the victims and transferred it into the machine to power it. Of course, this theory becomes problematic upon viewing said rays explode military vehicles, but I'm going to blame that on Rule of Cool until either I or another troper can expand on this.
 * A focused beam of electrons would have the effect presented in the film, violently vaporizing water which could destroy people and vehicles while leaving stuff like clothes intact(if ragged).

The aliens do understand microbiology
They just thought they had it beat, it was just a matter of one or several very specific Earthborn viruses or bacteria that ended up bringing them down. They'd already prepared for or deemed themselves safe from billions of other kids.
 * Alternatively, they knew all about bacteria, but had never encountered the enigmatic threat of viruses before, which it could turn out, are exclusive to Earth(or at least not universal). It's a stretch, but it's possible.

The ships themselves were implanted during the lightning attack
Rather than being buried there for millennia to be piloted by lightning-riding invading aliens whose technology would've likely advanced far beyond them, the tripods themselves were what the lightning implanted in the ground.

Spielberg movie: The reason why the Japanese defeated some of the Tripods, is because they used Giant Mecha against them.
In the Steven Spielberg movie the story goes around the Japanese took some tripods down. Since Japan is partially known for its large amount of giant mecha its possible they finally deployed them for real, instead of just using them as props for television shows.

The Martians accidentally took bacteria back to Mars.
The entire planet was soon engulfed with a terminal case of just about everything. Only the Martian children survived, still being young enough to adapt and regrow an immune system. Most of the Martian's knowledge and history was lost, but the machines - merely being extensions of the Martian brain - were still useable. When the children grew up, they realized that society would stagnate if they didn't learn more. They turned to Earth again, knowing that the attempt to conquer it was what nearly killed their entire race. Instead, they sought to learn from us and hopefully coexist in peace. For the past couple of decades, they've been sending scouting parties armed with nothing more than a book of general knowledge, and they're quite friendly (if a bit shy.)

Humanity has been one long Martian scientific experiment.
Especially in the Spielberg film, where the tripods are planted on Earth in advance of the attack. The Martians seeded mankind on Earth thousands of years ago to observe the rise of a civilization; now they're satisfied and the experiment is finished. Time to sterilize the equipment and put the planet back to the way it was when they started. The tripods aren't soldiers, they're exterminators.

The ending of the 2005 film was All Just a Dream.
The movie ends with the fall of the tripod. It would explain the totally unlikely survival of Robbie Ferrier.