And Shine Heaven Now/WMG

Zorin will be on the HMS Eagle, and Rip will be the one to kill Pip
The doujinkshi-ka already said that certain plot points will be changed, this one seems likely, particularly in view of Rip's popularity among the Shine fandom.
 * Rip being the one to attack Hellsing manor was proposed to Erin by Xuanwu a couple years back.
 * It should be noted that Xuanwu has proposed a lot of things.
 * Alternatively, the girl reading on the ship is Maggie Mui. She HAS been mentioned before, and it fits Joker's Paper Master theory. It's not too likely and I hope I'm wrong, but I can't get the idea out of my head.
 * Maggie or Yomiko.
 * Confirmed! Looks like its Maggie.
 * And the second part is now Jossed. Rip is in Paris.

All the fangirls from Shine will return to watch the final battle
Well, why not? This would be the ultimate fangirling they can do, and EVERYONE would be there, presumably.
 * A mass fangirl explosion as the conclusion was also proposed to Erin by Xuanwu the same time as the Rip attack. In that version, the fangirls would make everyone friends and they'd all co-exist happily.
 * Alternately, they'd start the ULTIMATE flame war. Except the fangirl war would look much cuter than the real one.

After Millennium attacks the United States, Stephen Colbert becomes president
Given Erin's love of Colbert, this would seem an obvious turn.
 * Negative, see the comic "The Eagle Of Hermes".

The shadowed man in Millenium is Donnie Nakajima.
It is entirely possible that Donnie faked his death and defected to Millenium, perhaps as a means of using that to stop the British Library.
 * Jossed, see 'Evil Jeeves' WMG.

The Man in Shadows is The Master.
Well, it would be just so cool! "Integra: Vampire Nazis? Could you be any more of a cliche? The only thing that would make it worse is if you threw in time travel. The Major: Well, actually..."
 * Aided by this line:


 * It's someone in pinstripes at least.
 * Jossed, see 'Evil Jeeves' WMG.

During the Battle of London, Integra will turn the Thames into a river of holy water.
Well, we've seen her ability to consecrate liquid, twice, when she used her own spit and then fire sprinklers. And the Thames is a pretty big river. Now...how to harness all that water to use against the army...
 * Possibly confirmed! Given that about half of these rumors really happened...

One of Millenium's plans is to go back in time and help Hitler win the war.
Stupid Jetpack Hitler.
 * Semi-Jossed, the linked page in the WMG above hinted that it was to help someone worse than Hitler.

Aziraphael and Crowley will help stopping the end of the world
Well, for the bookstore, naturally.

The Man In Shadows is a resurrected Hitler.
It's such an obvious guess, no one's thought of it!
 * Jossed, see 'Evil Jeeves' WMG.


 * Oh, and another thing.
 * I was thinking she was A little girl who has an INSANE amount of faith in her lord. It helps that the flashback looked kinda like her in Feb 25th 2010's strip
 * Jossed.  Meaning the   one is still possible.

Sister Kim is the combination of Yumiko and Yumie.

 * Ala Midii Une in Gundam Wing, Yumiko/Yumie are forced to work out their problems, thus combining into a third new and final personality.

The Man In Shadows is Julius Belmont
Erin has already shown herself willing to crossover series and mess with Hellsing canon. With regard to in-comic/game evidence, in the Castlevania series, Julius is said to have destroyed Dracula in the Castle War that occurred in 1999. There is a war going on, the year is 1999, and Dracula is fighting against the side of the war The Man In Shadows is currently supporting. And while normally you wouldn't assume Julius would be the type of person to associate with Nazis, keep in mind that the Paper Sisters aren't either, and Millennium managed to coerce at least two of them into the fight.
 * I see one problem with that. This is the 21 February comic, sans dialogue. In the summary below, Erin says that the Man In Shadows is from, or at least related to, a previous major crossover. As far as I can recall, Erin has never incorporated Castlevania into Shine (but feel free to correct me if I'm wrong). Incidentally, this does strengthen both the Donnie theory (Read or Die is the most crossed over anime with Hellsing here) and the Master theory (the Doctor made an appearance in "Shine or Die").
 * Jossed, see 'Evil Jeeves' WMG.

The Man In Shadows is the head of Dokusensha.
As evidence: The World According to Shine. Now, can someone that's actually seen Read or Die tell me who that IS, or is this one of those 'we never find out' tropes?

The Ghosts of Iscariot wanted Enrico to miss the point.
Consensus is that Enrico missed the point of the dreams and he's now on a crash course to making the future come true. But would he have even conceived of wiping Hellsing off the planet if he hadn't dreamed the dream in the first place? Quite possibly no, at least not in this stage, it probably would have been wiser to remain on the side, let Hellsing and Millennium have at it, and pick off the survivors. The future would have been a whole lot different then. The Ghosts of Iscariot therefore went, possibly at Sailor Pluto's behest, to talk to Enrico, indirectly goad him into attacking now, and preserved the future we know and love.

Kim is one of Yumiko's personalities.
No proof, but she IS a Suspiciously Similar Substitute...
 * I'm going to take it one step further. Kim is the original personality.

The Man In Shadows is the person worse than Hitler
In The Eagle of Hermes, one of the things Integra supposedly did was travel back in time to stop a person worse than Hitler. Given that about half the other events either has or will happen, there's a pretty good chance this one is true as well. And this character is inserted into the plotline, with no foreseeable use in the Battle of London. So his part will probably involve going back in time to alter history.
 * Jossed, see 'Evil Jeeves' WMG.
 * Not necessarily, all that this WMG says is that the Man in Shadows is worse than Hitler. Who's to say Jeeves isn't worse than Hitler?

The Man In Shadows is Hans Landa
As mentioned in the above WMG, supposedly Integra took on someone worse than Hitler. Who could possibly be worse than Hitler? Ignoring my default answer, since I put that WMG up already, I went with people who would actually have been alive in WW 2, and who would have had the actual cunning to win a war. Landa would fit the bill, he orchestrated a way to, surrender himself, and get rewarded for the spoilered part, with Karma Houdini (mostly) kicking in. Plus, stretching a bit, he could possibly be still alive in 1999, especially if he is enhanced in some way like the rest of the Last Battalion. Now, I fully acknowledge that this WMG is most likely Jossed, since Erin has probably had this planned for years and Inglourious Basterds is a relatively recent fandom. But hell, it's WMG.
 * Jossed,see 'Evil Jeeves' WMG.

The person worse than Hitler and/or the Man in Shadows is an evil clone of Arthur Hellsing.
So I changed tactics a bit. Instead of thinking 'who's worse than Hitler?' I thought 'what would the most epic opponent for Integra be?'. The obvious answer is an Integra vs. Integra battle, but there's one problem with that: how would the Last Battalion get Integra's DNA to make an evil clone? So I went the next step up: Integra's father Arthur.
 * Jossed, at least the 'Man in the Shadows' part, see below.

The Man in Shadows is an evil clone of Jeeves.
Walter gets first crack at seeing him, so what'd throw him off bad is that he is or resembles someone he loves. Jeeves was his father figure, sooo....
 * Confirmed! At least partially, see 8/29/10's strip!
 * Now the question becomes, is it the real Jeeves or a clone?
 * I-Jin. So close enough.

It's NOT Jeeves, it IS the Master, he just regenerated into Jeeves.
What? It's not impossible. Plus, we still have the hanging thread of time travel possibly unresolved.
 * Jossed.

Why is Jeeves working with Millennium?

 * He's just that damn evil.
 * He snapped when Bertie died and is willing to do anything to bring him back to life.
 * The answer: he's an I-Jin of Jeeves.

That's not Jeeves, it's an I-Jin of Jeeves.
As someone on the forum pointed out, it's plausible since Bertie had written books on his misadventures, with Jeeves playing a central part. Also, when
 * WMG confirmed, it is not Jeeves, repeat, not the real Jeeves!

The Sailor Scouts will defeat Doc.

 * The author seems like too big a fan to let this not happen.
 * Confirmed, yet an Offscreen Moment of Awesome: only one frame of Princess Serenity fighting Set with the Holy Grail is seen. (Maybe a future storyline will go into detail?)
 * Yes. Yes it will.

The identity of the Integra decoy

 * Yomiko is the obvious choice, since she claims to be on a mission and does not recognize Anderson yet recognizes Heinkel (and remember, they were both in Shine or Die).
 * Anthy. I don't know, maybe this is where she tracked Utena to, and depending on your continuity,.
 * Marian. Which is unlikely, since she's serving as Integra's bodyguard, but still.
 * Jossed already.
 * A regenerated Rani. Hey, who says Millenium is the only one who has plans with creating a vampire army ?
 * Haruka, aka Sailor Uranus. Blonde, good with a sword, we already know that according to Sailor Moon canon she roves the world helping defeat monsters... And she already has the right color pantsuit.
 * Utena. Ridiculously unlikely since she's vanished off the face of the earth apparently, but it wouldn't be the first time someone who has vanished has come back in an unexpected fashion.

Integra and Anthy are related
Well, Integra is of Indian descent, Anthy  appears to have Indian blood,

Jeeves is either the true Big Bad or The Man Behind the Man.
Just something I noticed,, if you look at the complete Triptych cover, he is the person in the center of it, and his strings are over the entire cover. Hell, the Major isn't even IN the picture. So maybe he's just manipulating Millennium for his own ends.

Jeeves brought Millennium
Okay, admittedly, this has been something that bothered me in Hellsing canon proper:  Shine could possibly have an answer:
 * Well...not necessarily jossed. While it's not the original Jeeves, the I-Jin could have retained the memories of Mina's remains and found a way to abscond them.

Timothy is a descendant of Milo Thatch & Kida from Atlantis: The Lost Empire.
The more I look at Timothy, the more similarities with Milo pop up. Plus, Kida as an ancestor would explain Timothy's Darkskinned Blonde looks. (I know this'll probably get Jossed in no time, but it's too good to pass up as my first WMG.)
 * The Doujinshi-ka's Inbox thread on the forums has Jossed this... sorta. Turns out Erin's never seen the movie, and thus says it is crack, but may or may not be correct.

D has two mommies.
Integra said that his parentage was complicated and Seras says after being asked what kept her that he doesn't get his speed from her side of the family, not to mention the fact that we saw them kiss. Could it be that their eggs were combined to create the first dhampir?