The frame narrative follows Zachary Ezra Rawlins, a graduate student who comes across a mysterious book titled Sweet Sorrows in his university library.

Sweet Sorrows appears to be a fantastical short fiction collection, describing a book-filled labyrinth called the Harbor on the shores of an underground Starless Sea, but Zachary instead discovers one of the stories to be a perfect description of a experience he had as a child, despite the book having been published before it happened.

Dorian warns Zachary that an organization called the Collector's Club is targeting him to retrieve Sweet Sorrows, confirming the Sea's existence.

He finds a third book, The Ballad of Simon and Eleanor, which describes two residents of the Sea who lived generations apart, but met and fell in love through a temporal anomaly in the Harbor.

Allegra is revealed to have been Mirabel's adoptive mother before she was overwhelmed by apocalyptic visions of the Harbor's destruction and founded the Collector's Club to protect it.

Mirabel admits to her identity as Fate, having reincarnated countless times after her initial death, but insists she can only indirectly influence events and that Zachary must choose his actions for himself.

Dorian survives the fall when he lands in the Starless Sea, revealed to be a vast ocean of honey, and is rescued by Eleanor, now a proficient sailor.

There, the characters from the collection hand him a living human heart recovered from Fate when she was first torn apart, and warn him against mysterious spirits and hallucinations that haunt the depths.

[4] McReynolds noted the focus on philosophy and metatext over a conventional plot structure, expressing difficulty with categorizing the novel in a specific genre and concluding that "it may not have given me all that I wanted, but it did give me something I appreciate.

[6] She doesn't find the main character compelling, but does praise Morgenstern's style, which "especially in the frequent Grimm-esque interludes, employs aggressively simple children’s literature syntax to describe outlandish settings that are either opulent or decaying.

Her skill at rendering these spaces is remarkable, the smells of smoke and honey wafting through stone corridors and nameless cats slinking along secret passageways....

As an ode to an aesthetic, however, it is marvelous, rife with stags carrying lit candles on their antlers, fallen cherry blossoms and story-sculptors who put their chronicles in clouds.

[8] Her overall review, however, is unabashedly positive: "What did work for me, deeply and wholesomely and movingly, was the whole affect of the book, its warmth, its helpless love of storytelling and beautiful, polished fables.

"[8] Kirkus praised The Starless Sea as "high-wire feat of metatextual derring-do... with mystery and passion inscribed on every page," citing the novel's ambition and prose.