On a fishing boat near Port Whale, a duck is recovered from the sea. It's Donald, missing not only his PK equipment and costume, but apparently his memory as well. All he can remember is a dreadful name: Davy Jones, the Devil of the Deep Blue Sea. Will our hero be able to recover his memory from the ocean and escape the titular Ulysses Syndrome? And who or what is Davy Jones?
- Admiring the Abomination: While it's actively trying to kill them all, Barnum still seems rather proud of his creation.
- Animal Nemesis: Averted, while Davy Jones is the main threat of the issue, PK doesn't consider him an enemy, just another victim.
- Bar Brawl: The Kaplan's bodyguard Biff stops for breakfast in a bar, a group of disgruntled locals attack him. Donald interferes, and in the following brawl bonds with Biff, who's revealed to be a nice guy despite his though exterior.
- Call-Back: Barnum mentions that they found the remains of the Evronian Invasion Hive near the coast of New Zealand.
- Catapult Nightmare: Donald has one in the beginning, when he wakes up in Port Whale.
- Defusing the Tyke-Bomb: In the end, Davy Jones and the whale sense each other's calm and pain respectively, which causes the shark to pacify itself and follow the other whales peacefully.
- Evil Is Not a Toy: The Belgravian's scientists tried to obtain the ultimate weapon by injecting alien material found on an Evronian hive with a giant shark. It went horribly wrong, and they're trapped by their very creations.
- Faint in Shock: Donald faints when Kaplan's vague description of what attacked his boat triggers some memories and a flashback of his encounter with Davy Jones.
- Father Neptune: Captain Taddeo Mackarel, mayor of Port Whale and a true seaman who's wise and reasonable, treating the sea as a huge, all-powerful entity that only tolerates people, Above Good and Evil. He's also well-versed in sea-related mythology.
- Hellish Pupils: A nightmare in the beginning shows Davy Jones with yellow eyes with a single slit pupil which splits into forming his name.
- Hoist by His Own Petard: Barnum wanted to create the ultimate sea-bound killer machine. So successful that now he and his two buddies are besieging him and his garrison inside the underwater facility.
- It Can Think: Davy Jones, on top of being Nigh-Invulnerable, huge and extremely fast, is also exceptionally smart.
- Improvised Weapon: During the Bar Brawl, Donald employs a tray as a shield. When Biff comments on it, he claims he "was spontaneous to him".
- Laser-Guided Amnesia: Donald spends half of the story with amnesia after his shocking encounter with Davy Jones and his near-death in the sea. Captain Mackarel compares it to the story of Ulysses, hence the title.
- Lightning Bruiser: What's best than a giant, homicidal shark? A giant homicidal shark which cannot be detected by most systems and can swim up to 70 km/h.
- The Legend of Chekhov: Mackarel tells Donald a legend of a school of whales which were summoned through a special whistle and kept Davy Jones at bay. During the climax, PK accidentaly summons the whales using the whistle to close a punctured spot, and the whales manage to "defeat" Jones, though not by violence.
- Meaningful Name: The Mad Scientist who created Davy Jones is named Barnum, possibly after the famous showman and circus owner P.T. Barnum.
- Nice Guy: While the mariners of Port Whale are highly suspicious of Kaplan and thinks of him as a good-for-nothing, greedy treasure hunter who's behind the disappearence of the fish and "Davy Jones"' attacks, he's revealed to be a genuinely nice and helpful person overall, who's not involved with the mess.
- Non-Standard Character Design: The waitress in the bar: it's hard to understand if she's meant to be a duck person with a really short, flat beak or if she's The Noseless with large lips and, for some reason, white skin.
- Out of Focus: One only comes back in action in the second part of the story.
- Pragmatic Villainy: Technically, the Belgravian's scientists are the bad guys there, and they know that they'll have to pay if they go back to the surface with PK, their enemy. OTOH, he's the only person who can save them from Davy Jones, so they won't try anything funny to jeopardize their safety.
- Reasonable Authority Figure: Captain Taddeo Mackarel is understanding, wise, firm and just, and won't tolerate uncalled provocations not even from his very citizens.
- Red Herring: Kaplan is introduced as a nosy, greedy treasure hunter who's despides by the people of Port Whale. He's actually a good guy and not involved with the disappearence of the fish.
- Shaming the Mob: When the fishermen try to accuse Kaplan during the town meeting, Mackarel scolds them for being so childishly angry and mistrusting.
- Threatening Shark: Davy Jones is a huge shark injected with alien DNA to become incredibly fast, though and smart, and is the main threat of the story, along two smaller mutated sharks he control. Despite everything, PK doesn't really consider him a monster to be destroyed, but a tragic victim of reckless science.
- Title Drop: When Mackarel calls Kaplan out for seemingly keeping Donald captive against his will, he tells him the story of how Ulysses was kept prisoner by Calypso and lost his memory until the gods restored it to him, drawing a parallel on how Donald's memory was "taken by the sea" and asking Kaplan if he expects to be as good as the gods.
- Tragic Monster: In the end, PK sees Davy Jones and his brethern as such. They're ultimately defused and accepted by a school of whales who adopt them and soothe them.
- We Need a Distraction: PK uses holograms of the Pi Kar to distract the sharks and leave the base. Unfortunately, Davy Jones realize that he's chasing a copy after he sees it phasing through a rock.
- You Don't Look Like You: Invoked but downplayed: Mackarel mentions that Davy Jones is usually described as a horrible creature covered in weeds and broken nets, but he claims that a devil can take any form he likes.
