In 3028 A.D., where humanity has mastered deep space travel and interacted with several alien species. A human invention called "Project Titan" alarms the Drej, (who the Daleks are working for) a pure energy-based alien species who attack Earth after breaching the Global Defense System. As the Drej and the Daleks start to attack Earth, Professor Sam Tucker, the lead researcher for "Project Titan", sends his son Cale and our heroes on one of the evacuation ships with his alien friend Tek and a anthropomorphic swallow named Wave while Tucker and other members of his team fly the Titan spacecraft into hyperspace. When the Drej mothership destroys the Earth with an energy beam, the surviving humans become nomads, generally ridiculed by other alien species.
Fifteen years later, Cale is working in a salvage yard in an asteroid belt at Tau 14 with Wave. Cale meets Doctor Aaron, Cynder, and Batty Koda and encounters Captain Joseph Korso, his female human pilot Akima and the alien crew members of the Valkyrie named Preed, Gune and Stith. Korso reveals that Professor Tucker encoded a map to the Titan in Cale's ring. Tek tells Cale that humanity depends on finding the Titan. When the Drej and the Daleks attack the salvage yard, Tek convinces Cale to go with Korso as Cale and our heros escape from the Drej and the Daleks. Cale realizes the Drej want him dead before he can find the Titan.
On the planet Sesharrim, the bat-like Gaoul interpret the map and discover the Titan is hidden in the Andali Nebula. Drej fighters arrive and capture Cale and Akima. The Drej eventually discard Akima and extract the Titan's map from Cale. Korso's crew rescues Akima while Cale eventually escapes in a Drej ship and rejoins the group. Cale's map has changed and now shows the Titan's final location.
While resupplying at a human space station called New Bangkok, Cale, Akima, Wave, Doctor Aaron, and his crew discover that the the Drej had payed Korso and his assistant Preed to destroy the Titan. Cale, Akima, and Wave manage to escape the Valkyrie with the TARDIS team's help but are left stranded on New Bangkok when Korso and the rest of the crew set off for the Titan. With the help of New Bangkok's colonists Cale, Akima, Wave, and our heroes salvage a small spaceship named "Phoenix" and set out to find Titan before Korso.
When they arrive at the massive ice field in the Andali Nebula and dock with the Titan before the Valkyrie arrives (which had secretly followed them). Upon docking with the massive vessel, they discover DNA samples of Earth animals and a pre-recorded holographic message left by Cale's feather in the event that the Drej had gotten to him first. Professor Tucker explains that the Titan was designed to create an Earth-like planet including the native animal and plant life thanks to stored DNA samples, but has lost the energy necessary for the reactor to start the process after its initial escape from Earth. The message is interrupted by the arrival of Korso and Preed. Preed attempts to double-cross Korso (who was earlier bribed by the Drej against him) but Korso kills him then attempts but fails to seize Cale's ring. Moments later, the Drej and the Daleks attack the Titan, but are diverted by the Valkyrie's remaining crew. Cale, Wave, and Doctor Aaron modify the Titan to absorb the energy beam fired by the Drej mothership aided by a repentant Korso who sacrifices his life in the process. The re-energized Titan vaporizes the Drej mothership and molds the asteroid belt into a new habitable planet titled "Bob" jokingly by Cale and "New Earth" by Akima.
While on "New Earth", Cale and Akima witness the planet in action. Stith and Gune leave on Valkyrie to another planet as they wave goodbye to their human comrades. Doctor Aaron and rest his crew with Wave joining them bid their futuristic friends farewell and depart on another adventure as human colony ships (including the New Bangkok) approach the new planet to start life anew.
- Wave the Swallow joins the TARDIS team.