Everyone in that house was in on the scheme except for Athena, and even she abetted it a little. It MAY BE that Marston wasn't in on it and his bewilderment on the stand about the contradictions was honest, but that requires some wacky coincidences.
The story begins when Athena got Simon Blackquill's name cleared for the murder of her mother. She thought him innocent, possibly because she (mis)read his heart. Then Simon prosecuted Arts in a massive scandal, and even though Arts got away, the scandal ruined him and left him a recluse. He may have been legitimately guilty!
Those who actually knew the case, however, were not convinced that the whole truth had been found. Mary Adair and Nathaniel Marston realized that something was missing - I don't know what - and kept digging. Meanwhile, Athena eventually realized that Blackquill, whom she'd defended on the stand, really had killed her mother, and killed him in anger. Apollo saved her.
Arts sent out invitations to Adair, Marston, and Blackquill - though Blackquill was dead, so the letter went to Athena instead - to act as a "jury," with his butler present as well. He had reasons for what he did, or perhaps he had been misrepresented. For whatever reason, Adair and possibly Marston decided to acquit him. And to do that, they would fake his death so he could take on a new life. Somehow, Marston felt bad enough about what had been done to Arts to be willing to go to prison to protect this imposture. It is possible - even likely - that Marston did actually shoot at him to complete the illusion; otherwise Apollo would have picked up lies in his testimony.
The vanishing body was, of course, a trick to bring Arts back to life under a new name.
* Arts scrubbed his identity as far as was humanly possible... save for some blood samples, the sort of thing that could be planted at a scene, then doctored a little to make it less obvious that they were planted. This makes sense if he wanted to fake his death, and also if he wanted to take a new identity.
* When Adair talks about the old case, she SEEMS to be suggesting that Arts did something awful. However, she is vague enough that the man who "controlled" events might have been Blackquill.
* It's implied that Athena lied on the stand to protect Blackquill for some reason. If she realized that he really was a murderer or a liar after he adopted her, this would explain... a lot, really.
* Arts always wore a mask. Handy for starting a new life.
* There's no way Arts invited three people over just to KILL him. So what were the three invited for? Some plan, which they were all expected to take part in. Later dialogue seems to confirm that they were all in on it, except for Athena, who is shocked when Marston won't allow her to get a re-trial even if she can "name the culprit."
* This is subtle, but Apollo refers to a "job application" and blood tests when discussing whether or not they arrested "him." My guess is that "him" is Arts, who was finally caught.
* An empty turnabout? One with no actual murder in it? Of course, that the BBC Sherlock series has an episode called "The Empty Hearse" (after the story "The Empty House") that had a faked death in it is probably pure coincidence.
* If Marston wasn't already in on whatever plot was happening, and just "happened" to try to kill the victim when this all went down, and genuinely believed himself to be guilty, there'd have to be a lot of dubious chance events and coincidences in play here.
Problems with this theory:
* APOLLO'S POWER. Given what's involved, he ought to have picked up more lies.
* Psychological implausibility. All over the place. Surely there are better ways to fake a death than willingly going to jail? Or making someone unwillingly go to jail, if Marston wasn't really in on it?