You guys are close in your replies, but not quite there. Here is what really happened...
- Did Danny actually kill that one cop, one of the two who came bursting in? He pistol-whipped him, but the gunshot is only shown discharging (nothing into the guy) and most of the reaction is from his wife when she hears it over the phone. If not (and I expect not) how is that resolved? Does the guy come to and come walking in or something?
No. Danny just fired a shot in the room. Later toward the end of the movie when Sabian comes up and talks with Danny in person, again, Danny shows him the cop, who is tied up and gagged but alive. He is rescued shortly afterward when Swat/FBI raid the building, even though Danny escaped.
- Who are the ultimate bad guys? What's their comeuppance, exactly?
Frost is the ring leader, and most likely the guy who actually killed Nate. He was on the disability fund's board with Danny, so he had access to the money. The other SWAT guys were involved, Hellman, Allen, Argento, they subbed false claims to get their share which Frost would cover up. They paid off Neibom and framed Danny.
- What was the scam? Taking money from the disability fund?
Yes. Rudy explained it in the movie. Its the same as insurance fraud, where you would submit a false claim and get paid out. But it would only work if the "agent" was in on the scam. The "agent" in this case would be Frost, where the SWAT guys involved were those submitting the false disabled claims.
And Neibom was involved too. He confessed this toward the climax of the movie. Nate lied about there being some other "informant" that he was meeting with. Nate himself was the informant who told Neibom about the scam. Nate worked for Internal Affairs, he worked directly for Neibom, but did not tell Danny because it was classified. When Nate told Neibom about what was going on, Neibom went to the SWAT guys and they paid him off to be quiet and help frame Danny. The night Nate was killed he was there to meet Danny, or at least he thought he was, because of the pager message that was sent to both Nate and Danny, presumably sent from the killer.
- What ends up happening (or not happening) to Danny?
Sabian and Danny trick Frost into confessing everything, using a bluff, where Sabian pretended to want in on the conspiracy. His confession is heard on cb radio by the entire force. They arrest Frost and the other guys involved, Danny is cleared.