The Queen was aware of the Asterite and how its aid to Ecco had led to her defeat in Ecco the Dolphin, though it is never explained how this knowledge was gained. Despite still having the injuries from her battle with Ecco on Vortex, the Queen successfully destroys the Asterite and scatters its globes across the ocean. The attack on the Asterite takes place during the Fault Zone level, wherein the environment shakes, large rocks fall upon Ecco, and Ecco eventually loses his powers.
The Asterite of Earth's natural future relays his memories of the attack to Ecco after Trellia brings Ecco to her timeline. The memories of the Asterite stop short of showing Vortex drones from the the dark future removing one pair of globes. Ecco only learns of this from an Orca in the Sea of Darkness who had witnessed the death of the Asterite. Despite the future Asterite making no mention of this interference by the future Vortex, the present-day partially-rebuilt Asterite makes several mentions of the stolen globes.
As soon as the Asterite is destroyed, Ecco's powers are lost and he is once again obliged to surface for air. In addition, in levels prior to the restoration of Ecco's powers, Ecco must charge-sing Vortex drones to damage them, rather than simply sing at them. Strangely, warrior drones are still affected by simple singing.
The Asterite's death was sensed by singers all across the ocean. Ecco learns of the Vortex invasion and sets off on a quest to retrieve the Asterite's scattered globes; one pair at a time. As Ecco pieced more of the Asterite together, it regained its ability to sing and informs Ecco of the need to complete its restoration so the dolphin could regain his powers and defeat the Vortex.
After collecting the Asterite's globes in the present and travelling to the Vortex future to retrieve the final pair, the death of the Asterite is essentially undone, and Ecco regains all his powers.