- The scene at the end of Shades of Grey where Danko finds the rabbit didn't lead right into the scene at the start of Cold Snap. At least one day passed between the two scenes. Two things indicate this. First, in the scene at the start of Shades of Grey, Danko is wearing a dressing gown and appears to have just woken up. Second, Sylar was already in the house during the scene in Shades of Grey and hadn't tripped the alarm getting in. This suggests that his tripping the Front Door alarm when he exited in Cold Snap was a deliberate action to get Danko to come out and find his "gift" right then.
- Additionally, there's nothing else in any of the scenes in Shades of Grey and Cold Snap which says that the one leads directly into the next today/tomorrow style. Indeed, your point that Danko wouldn't just go to sleep after finding evidence of a break-in - along with Noah Bennet's reference to more hacking attempts by Rebel we didn't see - suggests more than a few days passed between the two episodes.
- Also, Sylar's personal relation to the main story has been somewhat limited this season, with its' last interaction occurring when Sylar was tracked down in Building 26. It's entirely possible that the scenes from Sylar's storyline weren't occurring at the exact same time as the scenes involving other characters.
- The show has done this before and indeed it's the only way to fit in some of Matt's scenes in Season One.
After the incident where Danko attempted to fabricate a "real" terrorist attack by leaving a doped-up Matt Parkman in an explosive vest on the Mall in Washington D.C., Nathan apparently had enough evidence to convince The President that Danko was unstable and sign the paperwork to fire him and put Noah in charge. Danko responds to this by ambushing Nathan and Noah in the hallway, firing shots into a window and then pushing his now ex-boss out the now broken window.
There are a few problems with Danko's plan...
1. If Danko knew exactly what power Nathan had, he had no way of knowing whether or Nathan could trigger it in time to keep himself from becoming street pizza.
2. If Danko knew that Nathan could fly, he had no way of knowing that Nathan might die rather than use his power to save himself and reveal his secret.
- While Danko would definitely die to protect a secret, Nathan wouldn't and Danko probably knows this (if only through the logic of "he's not hardcore like me!")
3. If Danko only suspected that Nathan had a power and didn't know the exact nature of it, he had no guarantee that Nathan would be able to survive the fall using his power. Turning invisible isn't much use in fighting gravity.
- Danko almost certainly thought Nathan's power was flight, though; the part where Nathan ran up to "roof access" when he had to get somewhere was a pretty big clue. He'd also seen Peter demonstrate flight several times, and Noah had told him that Angela had it.
4. Even if Danko's attack was an unplanned act of rage (we can easily believe Danko is Ax-Crazy enough to try and kill Nathan and damn the consequences) and his outing of Nathan was pure dumb luck, I can't believe that accidentally outing Nathan as a powered human would automatically put Danko back in the good graces of The President. Nathan being a filthy mutant does nothing to alter the facts or charges against Danko, which now include attempted murder of a U.S. Senator as well was the myriad of charges that SHOULD be pressed against someone who attempted to fake a terrorist bombing with live explosives that could have honestly hurt real civilians.
- My guess is that Danko told the president Nathan was lying about everything he'd told him, and Nathan was trying to get Danko discredited because Danko was onto Nathan. Any other stuff that Danko did, he blamed on Nathan, and as proof that Nathan couldn't be trusted, offered up the fact that Nathan had started a program to contain the heroes while secretly being a hero himself.
- As for why Noah isn't in charge: My personal assumption is that Noah was a CIA agent before joining the Company, who left because he found out about the existence of posthumans and the government couldn't effectively deal with them. So going to work for a private interest (assuming the US monitored him in some capacity, which seems prudent) may have caused him to be seen as unreliable, whereas Danko was a loyal government agent through and through. And a crazy person, but apparently that's besides the point.
- He's amoral/sociopathic enough that he'd actually accept an order to set up extermination camps for people with abilities if the powers that be felt it necessary to take things to the next level (and contrary to Wildstorm comics, those kinds of people are not in massive easy supply in the US intelligence/special-ops community), along with having so many skeletons in his closet that if he ever tried to go to the press with what he knows, he'd have zero credibility — and, indeed, be the perfect fall guy for this entire "rogue operation". Add in that unlike most people found with these "qualifications" he's not an uncontrollable psychopath, and has at least moderate competence in his role as long as you're willing to accept a certain amount of collateral damage — and let's face it, any administration that would sanction this mess in the first place is willing to accept a lot of crap — this would make him a very useful choice. Sure, he's not perfect for it, but sometimes you just don't have Captain Perfect on the payroll and so you make do with what's available.
- He got hit with enough tranquilizer to drop an elephant. Good chance that he's dead, but either way it's not unreasonable to think he just didn't wake up for a while.
- Ah, okay. Something must have happened with my signal because last I saw, he and Bennet were looking at things through a computer screen. Didn't see the backstab attempt.
- Apparently, Word of God is that Danko is still alive and out there, but won't be used as the Big Bad of Volume 5. Presumably, "Nathan" finally convinced the President to have him put in a rubber room for all the crap he pulled.
- According to volume 5, he was killed by an agent of the new Big Bad
- Danko's entire life at this point has been pretty much ruined. He's probably really set on taking his frustration out on somebody, and Bennet just happens to be there.
- Also, at this point Bennet had outlived his usefulness to Danko. Danko no longer needed Bennet to escape, since Hiro had already taken care of all the guards and security locks. And Danko is doubtlessly arrogant enough to believe that, even after everything that's happened, he could take Sylar on by himself without needing Bennet or the Heroes (some people never learn, I guess).
