The basic question remains: What happened that night?
The huge likelihood: Rudy Guede broke in through Romanelli's bedroom window at around 8.40pm (having cased the whole house and found it unoccupied, dark and quiet), with the aim of stealing money, electronic goods and other valuables. He closed the external shutters once he was inside, thus obscuring evidence of his break-in from anyone outside. He went for a wander round the cottage, drank some juice, and went to defecate in the large bathroom, in the belief that he had almost unlimited time in which to work.
While he was on the toilet, however, Kercher arrived home. Kercher locked the front door behind her, removing the key and retaining it (the door needed to be locked otherwise it would blow open owing to a broken latch, and the key needed to be removed from the door in order to make it possible for others to unlock it from outside if they came home). At this point, one of several different things could have happened. My best guess is that Guede tried to exit silently through the front door, but found it locked, and came face to face with Kercher at this point. Some sort of verbal altercations ensued, which then turned to physical, and then sexual violence, as Guede became aroused by the situation. He forced Kercher into compliance with his knife (perhaps telling her that if she did what he said and didn't call out or struggle, he'd treat her well and leave quietly....), then initiated a sexual assault with her on all fours and Guede behind her holding his knife at her neck. I think that Kercher may have struggled and screamed out at this point, causing Guede to inflict the knife wounds to the neck.
I think that all of this happened before 9.30pm. I think that Guede then stopped, in shock and horror, and spent some time trying to figure out what to do. In the end, he decided to wipe up some of the blood with towels from the small bathroom, and to clean the blood off his own hands and clothing. He left just after 10pm, taking Kercher's phones with him. After Kercher's UK phone rang out to indicate an incoming photo message at just after 10.15 - while Guede was on his way home outside the city walls - he decided just to dump the phones and threw them away (where they landed in MRs Lana's garden). Guede then got back to his apartment, composed himself, and went out clubbing into the centre of Perugia in a conscious attempt to construct some sort of alibi.