Digimon Tamers/WMG

Alice is a ghost who returned to help her Digimon sacrifice himself to help the Tamers, then escort him to the afterlife.
As Alice walked away, the "remnants" of her Digimon accompanied her. They both vanished. Her father keeps a picture of her that he looks at with sadness. Even the Japanese producer of the series has commented on his webpage that this is a haunting theory.
 * You mean that there are other theories for that event?
 * You mean this is the default theory? I always figured that she couldn't cope with losing her partner and just ran away somewhere.
 * ALTERNATE BUT SIMILAR: She's in a coma, like Shibumi, and is able to project her image. Everything about the ghost theory (her sudden appearance and disappearance, Dolphin looking at her picture sadly) still fits. The reason she looks more solid than Shibumi is because she's a child, and as it's been established, the thoughts of children have a greater power.

All Digimon universes (each season after 2 being an alternate reality) are interconnected through the Digital World.
Explains how the first two season's exploits are shown in their entirety as a kids' show in the third, and how Canon Immigrant Ryo is able to help our heroes out.
 * It was explained in the games that there is more than one digital world, and they all work as alternate realities. They were created by Millenniumon during the events of the third game "D-1 tamers". All of the digimon-verses are interconnected, not through the digital world, but through Ryo and Milleniumon. Ryo is in the Tamers universe because of the events of the second and third games.
 * In the games, the common starting point of all Digital Worlds was the first computer, ENIAC.

The entirety of Season 3 was a massive Gambit Roulette by Ryo's partner/villain Millenniumon.
Having seen the future, Millenniumon realized that he would inevitably be fused with Ryo's digimon to create a new being -- which, incidentally, would end Milleniumon's independent existence. Being the time-traveling god-thing he is, Milleniummon helped mutate a dormant program of one world into an Artifact of Doom and influenced a government organization in that same world, all to create a device that would have the side effect of reverting a Digimon's data to a devolved state. This is exactly what happened in the end: all the Digimon reverted to Baby II/In-Training forms. This also reversed the fusion between Millenniumon and Monodramon, but Milleniumon made sure no-one was aware if it. Millenniumon himself is currently in hiding, not wanting to attract anyone's attention until it's too late.
 * Milleniumon is still Monodramon. Milleniumon is Ryo's true partner digimon, and the reason he did what he did during those games was to be Ryo's partner or else came from jealousy of the other digimon that Ryo had partnered with during his adventures. That's why Cyberdramon was so wild - it was two digimon in one. Milleniumon being behind the events in Tamers would undermine why he did what he did in the games in the first place.
 * Are we missing a few manuals here?
 * Yes.

Hypnos could have retrieved the kids from the Digital World more easily, but they wanted to do it in a way that would make it harder for dimensional passage afterwards.
Note how easy it was for the kids to get to the Digital World. Then Jeri creates gravity in the dimensional void by defining which way she thinks "down" is. The natural laws in the void between worlds are shaped by willpower. Hypnos later rescues the kids through a lot of brain-constipating rocket physics and programming and necessary travel vehicles to make later attempts to cross over encounter the same obstacles. Fat lot of good this did, though, because....

The Children are now Digital Humans, like Gennai from the first two seasons.
This is how Dobermon's sacrifice enabled them to fuse with their Digimon in the "real world." They're now partially made of digital matter. The Monster Makers made sure the Red Card didn't affect them (they're not going to banish their kids), leaving Digital Matter still on Earth, and so the dimensional separation wasn't complete. This is what let Takato summon the portal at the very end.
 * A side effect of this is that they probably no longer age. (They probably could appear to age if they willed it.)
 * Maybe they can't age without somebody hacking their data. After all, it seems that their partner Digimon couldn't age; natural (i.e. permanent) digivolution is equivalent to aging, and Calumon's Shining Digivolution had no effect on them; maybe they're stuck with that too. This could make the rest of their lives interesting.
 * I so support this.

An adult Takaishi Takeru is a Canon Immigrant who was pulled into the Tamers universe and took on the identity of Yamaki Mitsuo.
Yamaki looked a lot like a much older Takeru from Digimon Adventure 02. His growing to hate the Digimon in the Tamers world and his viewing them as embodiments of chaos and disorder and dangers to humanity may have come from his hatred of dark, dangerous Digimon as a child, which only festered because of all the hardships he would have faced after being torn from everyone he cared about when he was pulled into the Tamers world. He had a hand in creating Hypnos to make sure that he could protect people from the chaotic Digimon who may threaten them.
 * If someone is interested, there is a fanfic somewhere in fanfiction.net about this.
 * Interested. Link, please?
 * Lost Destiny by Firehedgehog.
 * One problem, tho'. How's he an adult when Ryo, also from the Adventure-verse, is still a kid?
 * Time-space distortion from travelling between universes? It happens in other universe-crossing sci-fi, so why not?
 * Hikari came with him. She's the kids' teacher.
 * Not possible, since the kids teacher (in the original version) cares only for her standing in the community, and chose to be a teacher because it was an easy job. Unless, thats how Kari really is...
 * Yes, I do like the idea that she's secretly a Bitch in Sheep's Clothing, while her goody-goody persona was only a mask. Or alternatively, because of her Big Brother Worship she has low-self esteem due to not reaching her own fractured idea of what/who she has to live up to, and transfers these feelings onto the community as a whole. Thus seeking approval from them, by becoming a teacher to gain a good standing within said community. Plus, she wants an that's easy after constantly having to deal with the pressures of being The Messiah, and saving the world every other day.
 * His girlfriend always reminded eerily of Yolei/Miyako. Which could have Unfortunate Implications...
 * Or, Given the Hikari theory above, OT 3 implications...

Jeri's dad is Yakuza
He's a big, heavy-set man who appears to own quite a large house despite being the owner of a rather sparsely occupied bar. Also, Jeri's mother died mysteriously. This was the original plan before the TV executives drop kicked that idea from a great height (Digimon being, you know, a kids' series), and there's no reason it can't still be true.
 * He seems inclined to deal with things sternly and seems somewhat inclined to physical discipline. It fits!
 * So this makes Jeri the Yakuza Princess, then?

Guilmon is the reincarnation of Season Two's Blackwargreymon, or some of BWGmon's data was mixed in when Guilmon was being born.
While Guilmon is a Virus type, he's very calm and gentle and doesn't much care for other Viruses; not caring for Viruses is reminiscent of BWGmon. When he gets angry, his eyes go all freaky and look just like BWGmon's.
 * They're even voiced by the same guy!
 * And didn't Takato design Guilmon to be better than Agumon? As in Blackwargreymon's rival?
 * Nope, the Diginomes made Guilmon, based on Takato's designs. He likely kicks himself later for putting a digital hazard on Guilmon, assuming the below wild mass guess is false.
 * That doesn't mean that the Digignomes didn't use Blackwargreymon's data.
 * Well, do remember that 02 happened in 2002, while Tamers happened in 2001... Note that Ryo left before 02. Besides, wasn't Black War Greymon's data used to make a barrier between the real and digital world? (not that it worked).

Jeri has some sort of mental illness.
The way she spaces out, reacts to people and things, and even her dog puppet (when she's already 11) are indicators that she might suffer a light mental problem, possibly one type of autism. It could make things a bit more interesting, since it's not normal to see mentally challenged people being portrayed in anime with a big role.
 * To be fair, Jeri's mother DID die when she was very young. This incident could have mentally traumatized her, which could explain some of her behavior to others.
 * I'd say Jeri is just a very, very, very mentally troubled kid. We should be thankful she's a good person.

Ruki's dad is a lolicon.
It could explain how a a mother can have a 10-years old kid and still look as young as her mid-twenties, to the point of still being a supermodel. Ruki's dad possibly got her when she was around 13 or something.
 * She was sixteen when she had her, so about 15 or so. Not Lolicon, but she certainly wouldn't be legal in most countries (including most of Japan).
 * That depends, the national age of consent is 13, though individual prefectures can (and do), make their own laws raising it as high as 18. Since we have no idea where she conceived we can't really know. Of course this only applies to the original Japanese. In the dub Rika is 13, so 12
 * Or, a slightly more legal possibility: Ruki is adopted. That would make it perfectly legal for her parents to have gotten her while her mother was only 15-18 years old. It would also help to explain some of the arguing and huge differences between Ruki and her mother, if they're not biologically related in any way.

Takato is the real Digital Hazard sealed in human form and Guilmon is his avatar.
Unlike the other tamers who found their partners, Takato created Guilmon from a drawing he made. There are two explanations for this that come to mind. Either there is something very different about Takato, or Guilmon was created the same way the Adventure digimon were. In other words, The Powers That Be of the digital world made our favorite bread-snarfing dino from Takato's data. This carries the unfortunate implication that from a programming standpoint, our little Gogglehead is identical to a digital Eldritch Abomination. Something that destroys the world simply by existing. Guilmon became Megidramon because of Takato's anger, but many fans noticed that Takato mysteriously gained a red Battle Aura identical in color to Megidramon's shortly beforehand. Coincidence?
 * The red aura could be of Growlmon digivolving into Megalo Growlmon, since immediatly afterwards, Megalo Growlmon comes from behind him to attack Beelzemon. Notice that Growlmon digivolved without digivice/blue card input. Just pure anger...
 * Imitatin' other Entries, there is a fic...It's on recommendations, look it up.
 * Please name the fic - it's not immediately obvious from the recommendations on the page.
 * Is it the fic, 'Dimensions'?
 * Well, in that sequence we also discovered that Guilmon's contracting eyes are a golden eyed version of Takato's Red Eyes when he's angry.
 * Also, note that the red eyes are not a natural eye colour; it's also unique, since his parents actually have brown eyes.
 * Also, in the CD message in a packet, the short story after the series, it states that Takato (who has no computer or computer skills), somehow manages to destroy a firewall designed to stop humans. Why?, because  i.e., he really wants to break through. To stop him they cover it with concrete.
 * So, he's Lain, as a boy?
 * Well, he doesn't have multiple personalities, but from the little of the digital hazard that was shown I would guess that he might as well be.
 * Further evidence: Nowhere on the original Guilmon drawing are there hazard symbols.
 * Guilmon was made by the Diginomes, based on Takato's drawings. As for him not drawing a digital hazard on Guilmon and breaking a firewall? I got nothing.
 * Takato is Lucemon sealed into human form.
 * Lucemon has blue eyes, that doesn't explain the red eyes. If Takato is a digimon sealed in human form, it probably is Chaos Gallantmon/Dukemon, who if I'm not mistaken actually has red eyes. Thus Guilmon (as Megidramon) would be his ride.

Ai and Makoto weren't invited to Ruki's birthday party for a reason.
Impmon and the Tamers wanted to limit the life-threatening drama they go through until they're much older. And the twins aren't happy about it.
 * I didn't invite four-year-olds to my eleventh nor thirteenth birthday party either...

Why we don't have Digimon.
Inside the show, it was speculated that the the D-Reaper was so advanced because it had come from another dimension. Now, since different dimensions each have a Digital World, then what if the D-Reaper had invaded the Digital World of our real world? That would explain why there aren't any digimon in our world... Note that it didn't invade the real (human?) world because it had not created J-Reaper.

Yamaki used to be a chain smoker.
Why else would he fiddle so much with a lighter?
 * In Episode 24, we DO see cigarettes in his office
 * He's still a chain smoker. In his office and at his house, his ashtrays are filled with used cigarettes. He just isn't seen smoking them onscreen.

The portal shown at the finale of the series was eventually used
But not in the series or audio tapes. After recieving messages from their Tamers, the Digimon would find their way to it and return. It's still there, they just hadn't used it yet. Well someone had to give a suggestion to give them a happy ending after that!
 * Not sure you noticed, but that portal was covered in concrete because Takato had almost forced his way in, so that portal is useless... That doesn't mean there couldn't be another portal, though, after the CD Drama Message in a pocket and original story ~with~ though.
 * True...but just because concrete can stop a human, doesn't mean it can stop a Digimon.
 * Let's not forget all the Digimon that bio-emerged WHILE that portal had not yet been dug up by Guilmon, from Episodes 1-13. And no one even said the CD drama had to be the ending of the English dub instead of Runaway Locomon (in which the portal presumably was used given that the Digimon are all back on Earth), some prefer the CD drama as the canon ending but it has also been argued that the main "canon" is the Japanese version, so if the dubs, including the English dub, are non-canon, aren't they their own universes and couldn't they atleast fit with the movie with no other place to go? (This troper of course will have a harder time making arguments for the Japanese version though but he is an English dub purist). IMO Runaway Locomon is the canon ending for the English dub, Takato and probably the other tamers used the portal to get there, reunited with their Digimon, less dangerous this time with the D-Reaper gone and Zhuqiaomon on their side now, Dolphin made another ark to send them home, and six months later... Locomon. (This troper has received many arguments from a potential arch-nemesis though)

Impmon's Champion and Ultimate forms are Devimon and SkullSatamon.
Since he warp digivolves, it's never shown on-screen just what Impmon's natural evolution line would have turned out to be. On the Digi Wiki, one possible digivolution shown for Impmon naturally is Devimon, and one for Devimon is Skullsatamon. Skullsatamon can digivolve into, you guessed it, Beelzemon. Now while there's no concrete evidence that this could be the case, the best proof is in the character design. Look how much Devimon and SkullSatamon resemble Beelzemon in Blast Mode. Beyond that, they're all Dark Digimon consistently described as "fallen angels", whom are Virus types, and in the Nightmare Soldiers family.

Taking this idea one step further, since Impmon was originally going to be Tamer's Big Bad, it's possible they were going to include Devimon and Skullsatamon as a Shout-Out back to the original show until the idea was jettisoned, leaving only Impmon's Mega form for the final product of the show.
 * Skull Satamon is a jogress and Devimon comes from Demidevimon. It is true that Digimon evolution has always been variable and since this is an "alternate universe" they don't have to Digivolve the same way but it would be weird to change those two. Just saying his other two forms are unrevealed makes more sense.
 * SkullSatamon being a product of DNA evolution means nothing in other Digimon 'verses. Take a look at later seasons where Armor Digimon show up as normal Digimon by the score, or Xros Wars where even some of the Legendary Warriors get included. "It would be weird" is no reason at all. And, funnily enough, in Digimon Masters, Impmon's Champion form is IceDevimon and his Ultimate is, you guessed it, SkullSatamon. Though personally, this troper's always liked Astamon despite his being Belphemon's Ultimate. It just makes sense with the suit and the gun and the head-thing, you know?

There IS a way for deleted Digimon to be restored.
It was just never said and/or discussed on the show. Besides, Dobermon's data got restored, so why can't the data of the other Digimon be restored?
 * Dobermon wasn't restored, he disappeared never to be seen again while Alice watched sadly. In my opinion the most interesting question is what is Alice, and what would it mean if she was a ghost. Is it that she is in a coma, like shibumi was, or is it that she actually died and remained a ghost?
 * Gorillamon seems like a much better focus for this theory. He could have been Not Quite Dead but since it was mostly off screen we have no way of knowing.

The Tamers series takes place in an Alternate Universe where the European colonial empires were much stronger...
...and one of them took at least a portion of the Middle East from the Ottoman Empire. The evidence for this is the fact that Kazu has what looks like the coat of arms of the Kingdom of Jerusalem, a Christian kingdom that ruled over parts of Israel, Syria, Lebanon, etc in the 12th century, and was apparently revived as a colony in the 19th century. Kazu, or someone he knows, must have visited the region on holiday and got him that t-shirt as a souvenir.
 * Kazu's t-shirt has the symbol for the Crest of Reliability (Joe's crest) on it from the earlier seasons of Digimon.
 * There are some serious differences between the symbol on Kazu's shirt and the Crest of Reliability. The crest looks like the British flag, while the symbol on Kazu's shirt looks much more like a Christian religious symbol, and somewhat like the coat of arms of the Kingdom of Jerusalem than does the crest of reliability.

The reason Cyberdramon is so strong and can Biomerge in the real world is Milleniumon
This seems kinda obvious. Milleniummon was Zeed Milleniummon at the time of the DNA Digivolution, and it would make sense that if he's still in there, he'd make it easier to fight with Ryo, hence the Biomerging. It also explains why Justimon is one of the most powerful Biomerges in the show aside from Crimson mode.
 * I have to disagree here. In the Cd Drama Message in a Packet, ryo states that he knew that he was made of data before returning to the real world, even though he doesn't specify exactly what had made him like that. On the other hand, Justimon is not one of the most powerful biomerges in the show. He doesn't even manage to destroy any particularly powerful agent (like that green one) by himself! In the final battle, he does manage use Sakuyamon's power... after both are nearly exhausted, thus the amount of power he has to handle is not even that big.

The D-Reaper is Missingno
The D-Reaper: a realativly simple computer program similar to different from the digimon that became a lovecraftian horror and tried to absorb the digital world. Hmmm, why does that sound so familiar?

The Partner Digimon All Die
The CD Drama's only logical conclusion.

The "other Dimension" that Shibumi theorizes D-Reaper might have interacted with is the Dark Ocean
Because all the eldritch stuff comes from there and we already know that the Tamers-Dimension is in the same Multiverse.