Conspiracy theories are a thing I have plenty of! Here are a bunch of them.
1. The Chairman is behind all the major events of the multiverse. I think that Pike is the driving force for the overarching plotline. I think that he bankrolls the baron (as a distraction and a source of tech), provides chemicals, weapons, etc to pretty much everyone, and is constantly searching for new avenues for personal power. The guy is immortal (for a given value thereof), and I'm thinking that he's willing to destroy anyone and everyone else in his quest. I wouldn't be surprised if he pops up again as the final bad guy, having attained cosmic-level power. If there is ANYONE willing to sell out the earth, turn it into grey goo, or upload his brain, its going to be Pike.
2. Mr Fixer is blind. None of his cards depict his eyes (they are either covered by the hat, or in shadow), and his new costume has no eye holes. this also explains why the Chairman revealed himself to Fixer in "Undivided Attention". He knew that even if Fixer survived, he would not be able to provide a physical description
3. Mr Fixer was killed (for a given value thereof) by the operative. He was kept barely alive by the Chairman as a bargaining chip, should other heroes come calling. He spent a lot of time in that place between life and death.
4. The other members of Dark Watch were the ones that took down the Operative (probably assisted by Parse, given the arrows sticking out of the Operative). Pike made a deal to escape by giving them back Mr. Fixer. This could possibly explain why Mr. Fixer looks younger, and the "bitter" part of Bitter Strike.
5. It is also possible that DW Fixer is a clone, grown in the biomimetic plasma vat. This could satisfy the statement that "if we ever see him without his hat, he's dead.
6. The Operative is Brave Thiago's mother.
7. Thiago is going to become Legacy (in name, if not power) when Pauline decides not to continue the Legacy name. It is entirely possible that Paul Parsons will also take on a new name, thus satisfying the statement that "there is only one Legacy"
8. Chrono-ranger is stuck in a time loop where he becomes plague rat. I know that there are a bunch of reasons that this doesn't work, but I like this too much to give it up!
9. Expatriette and Setback are an item as of Dark Watch.
9. Expatriette is developing powers, and her story is a 3-parter.
The first part is her with no powers, being driven away and experiencing prejudice. We see her getting a thrill from taking down super-powered people because of how they treated her.
The second part is the Dark Watch Expat. She's started to think that she has some sort of powers, but doesn't know their full extent. she certainly seems ridiculously hard to kill, and might even be coming back from the dead. she starts to re-evaluate the thrill she gets from taking down super-powered people (since she knows many good ones, and might be one herself). She becomes more thoughtful and hangs back to prepare instead of charging ins guns blazing (the shift from playing an extra card to aiming and sniper rifles). She also starts a relationship with Setback, and sees someone who (like herself) obviously has SOME sort of power. They help each other, and compliment each other's weaknesses.
The third part is yet to come. I think that Expat needs to confront Dawn on even terms, in the full bloom of her power. It seems like an important plot point for Dawn to see that she COULD have had the daughter that she always wanted (in terms of power), but drove her away with thesame kind of prejudices that Dawn experienced in her own childhood.
At least thats what I think.