I'm thinking along the same lines as Ferdielance here in saying that Ian Arts did indeed fake his death. It seems to be implied that Arts is Mary's younger brother, which would make her motives in manipulating the crime scene much more reasonable.
Anyways, long story short, Ian Arts took the place of his butler. Arts invited Blackquill and Marston in hopes that they would want to kill him. He was willing to let these two take the fall since, from his perspective, they ruined his life by prosecuting/testifying against him in the scandal case (from this we are to assume that he wasn't actually guilty).
He masqueraded as his own butler, and purposefully sent his own butler to his unknowing demise (perhaps he knew Marston was in the study and sent his butler in there to retrieve something, for example). Since it was dark, Marston did not realize that this man was not Ian. There was a struggle over the gun, but no fingerprints were left by the butler since he was wearing gloves. Of course, Ian and Mary lied about this fact by claiming he had no gloves. Marston's shot truly did connect, and the butler died. There were no tricks involving the other wing of the mansion.
Everyone heard the shot, and rushed to the room. Arts cleaned up the blood to hamper the impeding investigation (under the guise of keeping the mansion clean, of course). The blood found on the walls of the study was not a result of the struggle, but was planted there by Arts himself earlier that day (it was said that the blood had only recently dried). Everyone except Mary took Marston downstairs and kept an eye on each other. Mary disposed of the body into the abyss.
Now, here's where things get tricky. Why would Marston and Athena lie about Mary being in the room alone? A couple of possibilities for Marston:
1. Marston was already guilty about killing someone and didn't want to drag another down with him.
2. Marston genuinely believed that Mary hid the body to protect him, and again didn't want to drag another person down with him, especially a fellow police detective who seemed to be on his side.
As for Athena, she simply wanted the satisfaction of seeing Apollo squirm and fail. She could also later take the case (and the fame that would accompany it) herself through the retrial by presenting the fact that information was concealed.
Anyways, the "him" who got arrested at the end was Arts, of course. I'm not certain how, but either Apollo or Phoenix figured out what happened and had him arrested for his crimes.