The Vortex Queen is the main antagonist of Ecco the Dolphin and was the leader of a vastly powerful alien species known as the "Vortex".
In the original Ecco and his pod are swimming in their home bay. The Foe podmate challenges him to see how high into the air he can jump. When he is in the air, a waterspout storm forms and sucks up all marine life in the bay except Ecco, leaving him alone in the bay. Upon leaving the bay to search for his pod, he contacts several dolphins from other pods, who tell him the entire sea is in chaos, and that all marine creatures had felt the storm. After talking to an orca, Ecco travels to the Arctic to find a blue whale named The Big Blue. The Big Blue tells him such storms had been occurring every 500 years and directs him to the Asterite, the oldest creature on Earth. He leaves the Arctic and travels to a deep cavern where he finds the Asterite. Although it has the power to aid him, one of its globes is missing, and needs it returned. However, this can only be achieved by traveling back in time using a machine built by the ancient Atlanteans.
Ecco travels to the sunken city of Atlantis, where he discovers the time machine and an ancient library. He learns the cause of the storm; it was a harvest of Earth's waters that was conducted every 500 years by an alien species known as the Vortex. The Vortex had lost their ability to make their own food, and so every 500 years, they would harvest from the waters of Earth. Learning this, he activates the time machine and travels 55 million years into Earth's past. Ecco locates the Asterite in the past but is immediately attacked by it. Forced into battle, he manages to dislodge a globe from it.
This opens a time portal and he is sent back into the present. After receiving the globe, the Asterite grants him the power to turn his sonar into a deadly weapon against the Vortex, as well as the abilities to breathe underwater and to slowly regenerate lost health. The Asterite instructs him to use the time machine to travel back in time to the hour of the harvest. This time he manages to be sucked into the waterspout with his pod. Once inside the waterspout, Ecco makes his way towards the Vortex Queen, the leader of the Vortex race. Eventually, the Vortex Queen is destroyed and Ecco rescues his pod.
However in the sequel "The Tides of Time" Ecco discovers that the Vortex Queen was far from vanquished, and had, in fact, followed Ecco to Earth to build a new hive for herself. Ecco loses his powers from the Asterite early in the game, and soon after meets a dolphin with unusually long fins. She is his descendant, Trellia, and takes him to the distant future. In the future, dolphins are shown to have evolved helium sacs, and can therefore fly; they also display limited telekinetic powers. The ocean is said to have developed its own mind, as well as waterways that float through the skies (called the Sky Tides) apparently connecting all the oceans of the Earth. After exploring the future for a while, Ecco finds the Asterite.
The Asterite tells Ecco that when Ecco used the time machine to save his pod, he split the stream of time in two. One possible future for Earth is this bright, happy future of flying dolphins; the other is a dead, mechanical world, sucked dry by the Vortex. The Asterite refers to Ecco as "the stone that split the stream of time in two". The Asterite itself had been 'killed' in the past by the Vortex Queen; how it is able to talk to Ecco is not explained until later. The Asterite returns Ecco to his own time after their conversation.
Back in his own time, Ecco must piece the Asterite back together by bringing the globes that make up the creature back together. The final pair of globes have been taken by the Vortex to their future; Ecco must therefore go there and retrieve them so that the Asterite can help him defeat the Vortex once and for all. The Atlantean time machine is not an option as it only allows travel into the past. Ecco makes his way to the "Lunar Bay", which the Vortex have claimed as their own. Two Vortex drones then capture Ecco and take him to their future.
The Vortex future is shown to be full of strange machines, reminiscent of the final levels of Ecco the Dolphin. Ecco eventually locates the Asterite's last two globes held in a chamber called the Globe Holder. After freeing the globes from a bubble-chained holding device, another time portal returns Ecco to the present.
With the Asterite complete again, it is able to bestow upon Ecco the same powers that it had previously given him — breathing underwater and a song that can destroy the Vortex. It also calls all of Ecco's fellow Singers to help in the fight against the Vortex in the now-transformed Lunar Bay. Ecco himself fights the Vortex Queen after fighting his way through another crushing Vortex Machine; however, she again escapes, reverting to a larval state and bolting for the Atlantean time machine. The Asterite tells Ecco to destroy the time machine to prevent the stream of time from ever being split again. The Vortex Queen, arriving in ancient Earth after using the time machine, finds creatures she cannot rule over, and through the aeons, the Vortex are forced to simply integrate into the ecosystems of Earth as exopods and arthropods (ants, scorpions, roaches, crabs, lobster, spiders, etc). Ecco, instead of destroying the time machine, uses it and disappears into the Tides of Time.