The skeleton's ghost—a shy, homely girl named Emily—appears and explains that she too fell down the well and died of dehydration after breaking her neck ninety years ago.

As their friendship develops, Anya drifts away from her one friend at school, Siobhan, while Emily becomes disinterested in discovering her murderer's identity.

Anya later notices Emily becoming more controlling and adjusting her appearance by straightening her hair and smoking ghostly cigarettes.

After being confronted with the truth, Emily shows that she is capable of moving solid objects, implying that she put her finger bone in Anya's bag.

Anya stops and convinces Emily of the futility of her situation, causing the tearful ghost to dissipate, and the skeleton to fall back into the well.

Brosgol conceived the character of Anya when she was working on Put the Book Back on the Shelf (2006), a comics anthology based on the music of the Scottish indie pop band Belle and Sebastian.

She wrote a short story about a disaffected schoolgirl to accompany the song "Family Tree" (from the band's 2000 album Fold Your Hands Child, You Walk Like a Peasant).

She then used paintbrushes (being especially particular about her Winsor & Newton Series 7s) to paint on Canson translucent vellum atop her printed-out rough draft.

Brosgol inked the panels and speech balloons first, adding in the lettering digitally later with a custom font developed for her by John Martz; she colored the novel in Adobe Photoshop.

[10] Susan Carpenter of the Los Angeles Times interpreted the colors as "a subtle underscoring of Anya's bruised ego".

[13] Anya's Ghost was nominated for the 2011 Bram Stoker Award for Best Graphic Novel, but lost to Neonomicon by Alan Moore.

[14] The Los Angeles Times' Susan Carpenter reviewed the graphic novel and described it as "a well-paced story that feels dynamic and also intimate."

"[6] Whitney Matheson with USA Today wrote that Anya's Ghost is a "funny, creepy and a delightful page-turner" and cited author Neil Gaiman who called the novel "a masterpiece".

"[2] Almost six years after its publication, Paste listed Anya's Ghost as a comic having "the potential to mean something special, to offer something valuable and important, whether that’s revelatory depth or escapist fun, to a young reader.