Sometimes I have random moments of epiphany.

[fueschgast]

Yesterday I had such a moment again and I think I finally get what Sherlock meant by "Well/When I say friend...". I think it doesn't mean that the original owner of the skull was a friend of Sherlock, it probably means that the skull itself was sort of (because things can't really be friends) a friend. At least it did what friends do and listened to Sherlock's theories and stuff.

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[fueschgast]

I just had a vision of Sherlock interacting with Skull as if it's a person. I bet they totally celebrated birthdays and stuff (Christmas is even canon XD). Imagine Skull with a party hat and between its lips teeth a... that party noise thing with the name I don't know (unrolls when you blow)!

OH! You know how Sherlock sometimes keeps on talking to John, even though John's not there? That's probably because he was used to talking to Skull! Skull was always there, so Sherlock could always talk to it - he's not used to having a friend who sometimes leaves the apartment.