Reimu was really well-behaved, cleaning up her own stuff, being very independent. Heck, she even likes to drink canned coffee. However, there was a yukkuri disease going around, and because of a chance that the disease could mutate and affect humans, a city-wide extermination was conducted. Even pet yukkuris weren't spared.
Anon receives a syringe which is meant to put down pet yukkuris peacefully. Reimu is initially fearful, but when Anon lies to her for the first time, telling her that it's for the disease (which she knows about), she says she'll bear with it, in exchange for coffee afterwards.
After he injects her, Anon bids her goodnight as she's falling asleep. Reimu looks up at him, smiling tearfully.
"Yuyu! Onii-san! Goodbye... easy."
Anon wonders if she actually knew what the syringe was for.
Later, Anon finds himself buying coffee even though he never drinks any. He holds it so long that it warms up with his body temperature, and it reminds him of the warmth he felt with Reimu, the warmth he'll never feel again.