An introduction video shows Ecco the Dolphin using the time machine to travel back in time. The prologue to Tides of Time is reiterated for new players. The Vortex Larva is seen using the time machine, and it shows her appearing in a sea of darkness, where she dives down into the depths, to begin a new hive.
The games starts Ecco out in strange parts of the ocean, where he must struggle to find Atlantis. The first few levels would be a tutorial, with Glyph stones guiding him on his way.
"These glyphs were made for you to use. They will lead you back to Atlantis."
And intermittent messages about how to play the game would follow. Finally, when Ecco finds Atlantis, he is able to communicate to the Atlantians through a glyph.
"Who are you?"
"Only the chosen one may use these glyphs. Are you the one? The traveler through time has stars on his head like the ones in the sky?"
"We do not know where you are going or why, but you must use our machine to travel back to the place and time of our origin."
"We are at war with the planet Vortex, who even now threatens all life on this planet! Very soon we will commence our first attack."
"Our legends tell us of an ancient threat that the chosen one was sent back in time to destroy. You must go now, Ecco, and ensure our safety in the future! If we do not survive, the Vortex will surely consume all life on this planet!"
"Use this song, and go back now!"
So ecco uses the time machine to travel further back into the past, to before the time of Atlantis. He hears strange songs in far away waters, songs of Vortex kind. At the same time, he hears the familiar song of a friend, beckoning him.
In the next few stages, Ecco travels back through "Dark Waters", to find a young, but intelligent Asterite.
"Hello again, little one."
"I remember you from long ago, the little singer who took my globes. The sea is a very different place since then, and it has been a long time indeed."
"Ah! So that is why you had come! It is all clear now, though back then, I was not wise enough to understand the truth behind your visit!"
"There are terrible creatures in the warmer waters to the south. They are filling the sea with unnatural things, making the waters hot, and devouring all life around them!"
"If they are not stopped, all life on this planet will end!"
"They build great machines on earth, sea and sky. I will show you all I have seen."
The Asterite shows Ecco the new Vortex hive, a massive fortress rising into the sky. Ecco also has a glimpse of the Vortex constructing the Time Machine.
"Go back now, stop the creatures before it is too late! I will see you again someday, young singer."
Ecco has to travel into Vortex territory. Here, the sea is littered with Vortex. After a few levels of this, the Atlantians arrive in a great machine, and Ecco speaks with them.
"What has happened to the waters here, little one? Why do we sense the presence of Vortex kind?"
"Then it was we who sent you back, to warn us?"
"The Vortex have built many machines. We are weak from our travels, and we have no way of stopping them. The Vortex use crystal Glyphs to power their great constructs. If you can find five of these glyphs for us, we may be able to use the Vortex' own machines against them!"
"We will wait here for you to return."
"Hurry, Ecco!"
So Ecco has to penetrate Vortex territory once again. Similar to the globe holder stage, Ecco has to collect five of these "mini" glyphs, which will serve as the blueprint for the larger glyphs that the Atlantians will eventually create.
Before leaving however, Ecco comes across the Time Machine, protected by a Vortex Guardian, which would be one of the many bosses in the game. Ecco finds the last glyph in the time machine, which subsequently prevents the Vortex from using it. On his way back, Ecco runs into the Vortex Queen once again.
Working on the fact that in Alpha versions of TOT, the Queen could actually speak, we have possible dialogue options for her. This would go hand in hand with the fact that The Queen is highly adaptable, and has spent a great deal of time dealing with dolphins, so she might have developed some form of speech during this time. After Ecco kicks her ass, she might speak with him.
"It is you again, after all this time."
"No matter what you do, you cannot destroy us. You must know this now."
"We are an ancient race that has existed for millions of years. We are impervious. We cannot die."
"You have defeated us once again, but you will not leave this place alive."
The Vortex Queen Larva once again slinks off somewhere, and Ecco now has to escape a horde of vicious Vortex. He returns to the Atlantians with the glyphs, and tells them about the Time Machine.
"Thank you, Ecco!"
"With these Glyphs, we can now put an end to the Vortex menace."
"Return to the place of the Time Machine, and collect it's data with this device. Even if it is destroyed, we will be able to rebuild it."
"Hurry! Time is running out!"
So Ecco has to go back to the factory where the time machine was being built, and here, has one last run in with the Vortex Larva, who had planned to use the machine to travel back in time once again. Ecco defeats the larva, destroys the new glyph that the Vortex had installed, and speaks with the Queen once more.
"How is this possible? How is it that one like you could become so strong?"
"We had felt the presence of our own kind in the seas of your Earth, when we were forced to detach ourselves from the hive, and follow you back there."
"We had thought that we could start a new hive on Earth after coming back here. But now we see what we must do."
"You will never be rid of us, Singer. We will live on forever."
At this point, the Vortex Larva splits herself up into microbes, and dissipates. Ecco takes an imprint of the time machine, and escapes the hive just as the atlantians use their Vortex beams to destroy it. He travels back to the Atlantians once again, and engages in some final dialogue.
"Because of you, the waters are now free of Vortex kind. Thank you, Ecco!"
"Using the glyphs you have brought to us, we will ensure that you find us again. We have taken a sample of your life force. We will ensure that only you may use our Machine, and that we leave clues behind to guide you. We will be certain that you are able to save our world in the future!"
"The name Ecco will be embedded in our legends. The sea will sing of your name forever!"
This not only ensures that Ecco will come back to this point, but also that the Atlantians will know just who they are sending back in the FIRST game. (The time machine recognized ECCO specifically.) Again, Ecco does not tell the Atlantians of their destruction, as this would ruin the paradox. The Atlantians eventually charge up new glyphs, and use the Vortex technology to attack planet Vortex. The Vortex retaliate, and destroy Atlantis.
Finally, Ecco travels back to the Asterite.
"You have done well little singer. The waters of Earth are safe once again!"
"My powers are limited, but I have enough strength to send you back to your own time."
"Good luck, Ecco!"
The Asterite sends Ecco back to Atlantis, where he is able to watch the Vortex Larva use the time machine after sampling Ecco's DNA. Ecco then destroys the Time Machine properly, and returns back to Home Bay, for a fitting end.
Related: Alternate Ecco 3 Theory Part One
