The eco shortage was a catastrophe in the world at the time of The Lost Frontier. It involved the sudden shortage of eco due to an imbalance at the eco core, which caused massive eco storms, making the world's atmosphere grow unstable. It was an event which resulted in substantial damage to the world, and also made eco channelers such as Jak's transformation excruciatingly painful.
In the events of The Lost Frontier, Jak, Daxter, and Keira were sent to the Brink in the search of a new source for eco, presumably in response to worsening storms. After repairing the eco seeker, they were led to the eco core, a hot spot for the distribution of eco. After the re-alignment of the prism in the core under the old Aeropan barracks, the residing storms were calmed, to which Keira implied that the storms were accompanied by quakes, as both reduced in severity after re-alignment. The core's panel was able to remotely track and stabilize weather patterns on the surface once again, ending the natural disaster.