I recently found a rather interesting blog post, by Tumblr user riseuplikeangels, that discussed the possibility of a relationship between Charles and Sir of Lucky Smells Lumbermill. The blog post, transcibed below, can be found here.

A Series of Unfortunate Events, a series aimed (however sardonically) towards children and young adults, has a canon same-sex pairing, hinted at on such a minuscule scale you wouldn’t know it was there if you weren’t squinting, as well as reading another work inspired by the Series: The Beatrice Letters.
In “The Miserable Mill,” Sir and Charles are portrayed as business partners, but as the series goes on and as the canon is extended, we begin to see the true extent of their relationship. In “The Penultimate Peril,” Charles tells Sir that he cares about him, to no reciprocation. At the end of this twelfth book of the series, during the fire destroying the Hotel Denouement, Sir and Charles are running through the smoke, holding hands.
Their relationship is brought, still subtly, to the forefront in a section of “The Beatrice Letters,” where Snicket, in a series of metaphors that he uses to tell Beatrice exactly how long he will love her, includes the following:
“I will love you until C realises that S is not worthy of his love.”
Putting a gay pairing in a book series aimed at children? Making it quite literally not a big deal? Making it natural canon instead of a big well-to-do? Four for you, Lemony Snicket. You go, Lemony Snicket.

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