Eco Absence is the whole plot of The Lost Frontier -
The game begins with Sky Pirates attacking Jak's Hellcat on the way to the Brink. While Daxter manages to gun down two of the ships, daxter shoots the Hellcat on accident. Captain Phoenix and another pirate drop onto the Hellcat and, after they demand Eco, a fight begins. The unnamed pirate is tipped. On Brink Island, Jak and Daxter need to find a source to repair the Hellcat. They later find an Eco Prism to give the Hellcat power. When they take off they have to fight off Sky Pirates that are attacking the ACS Behemoth. When they land on the Behemoth, Duke Skyheed introduces himself and invites Jak, Daxter, and Keira to the Grand City of Aeropa. While in Aeropa Duke Skyheed and the Chancellor give Jak the Eco Seeker to see if he can power it. However, he fails due to the amount of Dark Eco in the area. Keira then asks if she can study it. The Chancellor agrees to let them see it for a week if they pass the Danger Course.
When Jak and Daxter have proven themselves in the Danger Course (and after Daxter escapes from the underground of Aeropa, now armed with a new form called Dark Daxter, due to further exposure to Dark Eco), Duke Skyheed and the Chancellor give Jak the Eco Seeker. Then, Captain Phoenix attacks the building and steals both the Eco Seeker and Keira. Jak and Daxter then chase Phoenix but are led into a trap, resulting in them landing back on the Island again. On the Island the duo meet The Castaway (later known as Tym). The Castaway automatically knows that Jak has been touched by Dark Eco. When Jak asks what his name is, The Castaway says he can't remember. He also mentions that he built the Robots. Jak then asks if he can repair his Hellcat and The Castaway says that in order for him to fix it, he needs a Velonium Power Pod from an Uberbot-888. The Uberbot-888 is the most dangerous robot The Castaway ever created. After Jak and Daxter get the Power Pod, The Castaway fixes his ship and sneaks on board. When Jak and Daxter take off they destroy the Phantom Blade's engine and defenses, causing Phoenix to let them land. On board Jak and Phoenix get into an argument, but Keira intervenes and makes them shake hands.
When Jak finds out that the Eco Seeker is missing two parts, they travel to Fardrop to get the first piece from a Pirate Lady. When they travel to the Old Aeropan Barracks, Jak comes across a testing table (similar to the one he was experimented on in Jak 2). He realizes that someone has been experimenting with Dark Eco and angrily states that whoever did it should be destroyed. When they find one of the Coordinates, The Castaway reveals that he is (or once was) a Dark Eco Sage and that he built the facility for the Aeropans. Phoenix reveals that he was once the commander of the Aeropan Air Forces. He was put in charge of a secret weapons program to make a new class warrior (similar to the Dark Warrior Program). When he found out what they were doing, he refused and tried to stop the program, but Skyheed wouldn't hear of it. So, he took the only option left and kidnapped the program's chief scientist (The Castaway) and marooned him on Brink Island to hide his work from the Aeropans.
When the location of the third coordinate sphere is found, the duo fly the Phantom Blade to Sector Zero. Jak and Daxter get the third sphere, but the Behemoth attacks the Phantom Blade and Jak has to defend it. Back on board, Jak, Daxter, Keira, Phoenix and the crew fix the Eco Seeker, which points to the Abandoned Research Rig. Then Phoenix recalls that the Research Rig was built over strange formations. It is then revealed to be a Precursor facility from long ago. When they reach the Eco Core, Keira tries to fix it. Shortly after, Klout shows up with Skyheed at the Eco Core, but was paid off by Skyheed in exchange for the location. Skyheed orders Klout to kill everyone excluding Jak, because he wants to study his unique ability to control dark eco. When Klout advances, Keira presses a button to activate an energy field with the Eco Core. The Eco Radiation kills Klout while Jak, Daxter, Keira, and Phoenix escape, leaving Skyheed behind.
Back on board, a message is sent stating that the Aeropans have laid siege to the Far Drop. Jak and Daxter are sent to defeat Aeropan Shock Troops attacking Far Drop. Then the Behemoth appears to destroy Far Drop. Jak and Daxter successfully destroy the Behemoth's weapons, causing the Aeropans to retreat. On board the Phantom Blade, Phoenix wants revenge on Skyheed for the attack. Then another message is transmitted anonymously, telling them to use the old Baracks warp gate. Jak, Daxter, and Keira get through the warp gate and Jak's Gunstaff weapons are disabled. Jak then has to destroy the Weapons Control System to use his weapons again. When Jak's Gunstaff begins to work, he heads up to the palace to defeat Skyheed. When Jak encounters Duke Skyheed, Skyheed begins to draw on mass amounts of Dark Eco that transform him into a Dark Eco Monster. Jak tries to defeat him but Skyheed escapes on an Airship. Jak then takes an airship and chases him but Skyheed leads him into an obstacle course and Skyheed retreats to the Behemoth to take power from the Eco Core.
Jak then has to stop the ACS Behemoth from stealing Eco Power from the Eco Core. Shields surround the Behemoth but the Phantom Blade disables them. When Jak destroys the Eco Crystals on the Behemoth. Phoenix flies the Phantom Blade between the Eco Core and Behemoth to prevent them from taking eco. But unfortunately the Phantom Blade gets destroyed and as a result, Phoenix gets killed. However, the Behemoth is now vulnerable to attacks. Keira then installs a Light Eco Beam in the Hellcat to finish the Behemoth off.
When the Behemoth is finally destroyed with Duke Skyheed, all of the Eco returns to the Eco Core making it balance again. Keira then activates the Eco Core and the Core channels energy which travels to Eco Vents around the world ending the Eco shortage and reduces storm and quake activity in all directions. Keira then channels eco energy for the first time. The Castaway then reveals his name is Tym. Keira then tells Jak that she and Tym have been decoding the symbols at the Core and that the circles at the core are attached to other energy lines. Keira says they have some exploring to do. Then Keira and Jak end the game by kissing and Daxter bragging on about bringing several things with him on their next adventure (such as a barf bag, magazines, snacks, etc.).
That is the plot of the game.