The story contains three protagonists: the titular Cilia herself, her husband Raymond Spike who is the secondary narrator, and their friend Zackery who is primary narrator. The latter two were crew members of the "Davey Jones", a ship that sank on April 12, 1872. While Zackery went out from shock, Raymond, the captain, took care of him on a makeshift raft, but would've been unable to keep him alive if not for their chance meeting with Cilia, a cilophyte, who had gotten lost in the same storm that downed the "Davey Jones". She comes to take care of them while they're adrift, providing food and medicine until they reach the shores of Kenya. By this time, she and Raymond have fallen in love and she agrees to marry him and join him to England while Zackery recovers in Kenya. The new couple's happiness only gets to last for so long, as the local fishermen catch on to the fact Cilia isn't human and come together to end her. They strike mere hours before Zackery arrives to meet his mystery savior, but Zackery is the one to find an unconscious Raymond and watch over him until he awakens. Raymond fills Zackery in about all that he doesn't know yet and the two go to find Cilia. They are too late to save her, however.
"Cilia" provides examples of:
- Cruel Mercy: The firshermen let Raymond live only to send him a note that reads: "Fish should be fried. If you want your fish, look for it in the old lighthouse."
- Downer Ending: Cilia gets tortured and mutilated beyond the point of possible recovery. On her request, Raymond kills her. Unable to live like this, Raymond drowns himself in the ocean while holding Cilia's corpse. Cilia gets avenged through her murderers' destruction, but that doubles as a reminder that she never returned home since the storm.
- Humans Are the Real Monsters: Type Van Helsing Hate Crimes. Cilia, while instilling horror in humans by virtue of what she is, is said and shown to be as gentle and kind a soul as there ever was. In contrast, most of the humans in the story, who only view her as a monster, are stonecold torturers who even have the nerve to party after their deed.
- Interspecies Romance: Cilia, a cilophyte, and Raymond, a human, are married.Raymond: "You see, we owe her our lives and I... I owe her so much more. It seems bizarre that I could love a creature so different from me in form, but I do."
- Love at First Sight: Averted, and with a note of dark humor to boot.Raymond: "The fog parted as we drifted closer and the first time that I saw my beloved Cilia, I was revulsed in horror."
- Meaningful Name: Raymond's ship is called the "Davey Jones". Zackery points out the ship's unfortunate name by saying that "the "Davey Jones" had gone to her namesake."
- Mercy Kill: Mutilated and in deep pain, Cilia asks for Raymond to kill her, which he does.
- Mood Whiplash: As this comic was published while Vampirella still was the pun-happy hostess of the magazine, she delivers a few jokes at the end of "Cilia" too. However, because "Cilia" is one of the rare comics of its type that goes specifically for tragedy, for instance by opting to end with Raymond's calm suicide instead of the killers' satisfying deaths, the jokes are a rude awakening.
- Our Mermaids Are Different: Cilia is an octopus-based mermaid. There's only one picture that shows off her lower body and, while the angle leaves room for interpretation, it appears that instead of a "normal" octopus-based mermaid, she is a twin-tailed type mermaid with each "leg" ending in three tentacles (her arms, presumably, count as the remaining two).
- Power of Trust: Raymond and Cilia are adamant about keeping Cilia's not-human-ness secret, but they do believe Zackery, who was not conscious during the time on the raft, has the right to know who saved him. They also believe he can be trusted to accept her as a friend and not tattle on her. They were right.
- Roaring Rampage of Revenge: Raymond and Zackery couldn't ever hope to get revenge for Cilia, but they weren't the only ones to love her either...Zackery: "As to the fate of Cilia's killers, there is nothing more than rumors. If you can believe them, the story is that after their crime, they held a party aboard one of the men's fishing boats. Some say their ship struck an underwater boulder and that the men were too drunk to swim to safety. Perhaps, but the wounds on the bodies recovered suggest... that Cilia's family had not forgotten her!"
- Shout Out: Zackery compares "the infamous cruelties of the Marquis de Sade" favorably to what has been done to Cilia.
- Sole Survivor: Zackery becomes this after Cilia's and Raymond's deaths.
- Spell My Name with an "S": As noted above, this story is the origin of the terms "cilophyte" and "cecaelia". "Cecealia" is not used in the story, but may have developed from faulty memories of the title: "Cilia". Meanwhile, while "cilophyte" is used, it's intended etymology is uncertain. "-phyte" is recognizable enough as "-growth", but "cilo" can come from "cilium" (plural "cilia"), Latin for fine hairs bundled together in a way that Cilia's tentacles can be argued to look like, "Scylla", the sea monster from Greek mythology, and "chilo-", a Greek-derived word better known as "kilo-" and meaning "thousand".
- Torches and Pitchforks: A marine version of it, featuring clubs, nets, harpoons, and lanterns. It's the fishermen who come to treat Cilia as the fish she is.
- What the Hell, Hero?: The heroes more or less call themselves out. Raymond chooses to tell Zackery about Cilia before they go save her because he feels it's necessary. When he is finally done, a message from the fishermen gets harpooned to the door. In response, Zackery exclaims it's "already noon" and that they've been talking "for a long time".