Okay this theory is expounded in a curious book that I have just read entitled 'Who Was The Man In The Iron Mask?' by Hugh Ross Williamson. I know that it sounds like a load of old rubbish, but it was actually an interesting work that attempted to provide solutions, based on evidence and theories as to the possible conclusions to historical mysteries.
The theory about Darnley's murder is this. The latter intended to kill Mary and rule as regent for the infant Prince James with the aid of Moray. He intended to escape from the house before the explosion, explaining that he had not had time to warn the Queen, who had been staying there with him. His clothes, including his cloak were taken into the garden by Taylor, his page, before the 'escape'. Up to this point all was going to plan, except that on Mary's last visit to Kirk o' Field, Paris, one of Bothwell's French servants who had just entered Mary's service had discovered the gunpowder that Darnley had put there and had told Bothwell. Bothwell prevented Mary from returning to the house that night, in spite of Darnley's almost hysterical insistence that she return and which she had promised so to do. Bothwell came himself to Kirk o' Field that night to watch events and possibly fire the gunpowder himself, unaware of the other plot to kill Darnley.
Darnley hearing noises outside the house, and being alone except for Taylor, made an attempt to escape only to be caught and suffocated by the Douglases in revenge for his betrayal of the murderers of Riccio.
Bothwell returned, determined to pay Darnley in his own coin for wanting to kill Mary, unaware that Darnley was already dead, and lit the gunpowder.
This would explain how the gunpowder got into the house - how could Darnley or his servants not have noticed previously ?- the method of death and the location of the bodies, and the destruction of the house.
It is entirely possible that the real architect of this was Moray. In the murder of Riccio, in which the Queen was the real target, Darnley was his tool; at Kirk o'Field it may be assumed that the same is true again, excepting that Darnley was hoist by his own petard.......Just a theory........