The Phantom Sub is the twelfth episode of the first season of the animated series.
"Does a ghost sub sail out there somewhere in the ocean? Ant believes it does, but when he actually finds it, the truth is even stranger - and much more dangerous."
Ant And Fontaine are out cleaning seaweed from the Aronnax's engines in the Rover (with Jeffery for company) when a strange object appears moving towards them which doesn't appear on any instruments, Kaiko is able to move the Aronaxx to avoid a collision (hitting a cliff wall in the process), after it passes by the object vanishes Ant believes it to be a ghost sub.
Back at home base Professor Fiction inspects the damage and calls the Nektons mechanical expert Lester for assistance, Ant describes the supposed ghost sub to Fiction stating it to be made of wood, glowing spots, and a large mouth that sucks in water, this reminds Fiction of something he read before and heads to find it. Lester arrives along with his son Griffin, Ant talks to him about the ghost sub, Griffin wishing he had adventures like Ant. Later Fiction shows Ant what his story reminded him of, the sailor Alessandro de Salazar a scientist who was persecuted for his wild theories, his last invention was a submarine called the Consail which disappeared on it's maiden voyage, Ant confirms it was what he saw.
In the study Will and Kaiko give Fontaine an assignment on the navigational theory she's been "supposedly" studying, wanting her to better understand the principles of navigation and to be ready if modern technology fails, Fontaine accepts. Early the next morning Ant has a dream where he sees the ghost of da Salazar and gets trapped in bubble and must find balance, Griffin wakes Ant up and tells him that theirs something on the other side of the island that he should see, Ant agrees and they take two Solar Skis out to see it, when they find it the object turns out to be the Consail, as they approach it the Consail starts to move towards them, in a panic Ant turns back but Griffin is unable to start his Solar Ski and jumps off and is swallowed by the Consail, Ant witnessing this pursues it.
Meanwhile Will wakes Fontaine for her assignment, he tells her that Kaiko is in the White Knight somewhere offshore and that she has one hour to find her using old navigational techniques using a rowboat to reach her and that she can't use her communicator unless it's an emergency. As Fontaine heads out Will receives a call from Ant who tells him that the Consail took Griffin, Will is confused, suddenly the Consail starts to dive and Ant jumps on it and gets inside and finds Griffin but is unable to call back, Will puzzled heads to the Aronaxx to investigate. Griffin explains that he was sucked into a pipe and hit a filter but was able get out from a hatch, realizing their trapped the Ant and Griffin then start to wonder who's driving.
Will finds the book about the Consail in Ant's room when Lester arrives and tells him that he can't find Griffin and that two of the Solar Ski's are missing, Will tells Lester about Ant's last massage and they both head out to search for them, while leaving Will tells this to Kaiko who is on standby if they need her. Back on the Consail Ant is unable to contact Will because of the thick varnished wood hull. Will and Lester find the Solar Ski's, Lester is really concerned since he never let Griffin swim. Meanwhile Fontaine is getting the hang of the navigation but accidently loses her sextant and compass (falling out of the boat in the process). Ant and Griffin head to the front of the Consail where they see what looks likes de Salazar himself but just turns out to be a coatrack, Griffin finds a book detailing the Consail explaining that it's water powered like the Aronaxx but the water level doesn't stay consistent explaining why it sits still sometimes.
As the sun rises Fontaine tries to get back into the rowboat but sinks it. Back on the Consail Ant and Griffin see the ship steer itself around a rock, Griffin finds out that the ship detects changes in the water pressure, explaining how it avoided collisions over the years, suddenly they see the rowboat as it sinks and see Fontaine above them, their able to stop the Consail and make it rise to the surface where they pick up Fontaine, once aboard the sub dives again. Fontaine remembering the navigational theory knows where to find Kaiko, Ant turns the Consail on the correct heading but it suddenly starts diving fast, Ant realizes that de Salazar designed the sub for himself alone and that the weight of three people has disrupted the balance, remembering his dream Ant tries to "find balance" by pulling a lever and they level out but are unable to pull up because of the flooding water, Griffin is able to activate the pumps and they surface. Once at the surface Will and Lester arrive along with Kaiko.
The Nektons bring the Consail back to base and the book Griffin found was actually da Salazar's diary, upon reading it Ant finds out that da Salazar himself was a Nekton. Fiction is excited to study the Consail only to find it has vanished, Fiction exclaims it to be impossible since they turned off the Consail's engines but Ant says that science doesn't apply to ghosts.
- This episode marks the first appearance of the Solar Skis.