Arglefumph plays a fan translation of the second Miles Edgeworth game, only released in Japan. The game's full title is "Ace Attorney Investigations: Miles Edgeworth: Prosecutor's Path". This is Episode 2, "The Imprisoned Turnabout".
In this video, Dogen says that his dog has been trained to clean up bloody crime scenes. This allows Edgeworth to transition to the topic that he should have led with: there is a hidden tunnel inside the prison, which the dog used to move the victim's body.
Judge Gorgeous brings out an autopsy report, which says the victim died from stab wounds in the neck. Was she hiding this evidence on purpose?
Edgeworth feels sad that his theory was disproven, so everyone gives him a pep talk.
Anyway, the autopsy report doesn't change the storyline THAT much. The dog still attacked the victim in his cell, then moved his body through a tunnel. The only difference is that Knightley was alive but unconscious for all of this.
So Knightley was killed, when his body was taken to Dogen's cell. Presumably, the murder weapon is Dogen's missing chisel.
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