Several paradoxes already exist. The only real way to really tie up the Ecco series is to consider what has happened, especially with the fact that, in the Ecco universe, events rely on one another, and therefore, cannot be changed.
Taking that into account, Ecco could not destroy the time machine BEFORE himself and the Vortex Larva use it in the Tides of Time.
So in my "Ecco 3", Ecco returns to the past, long before the Atlantians have been destroyed. They are at war with the Vortex world, and for reasons unknown to him, they have been given specific instructions on how to proceed with plans related to his journey.
Ecco is told to use their time machine to go back even further, to before the time of the Atlantians. Here, the Vortex Queen has started a new hive. Not only that, she is constructing the TIME MACHINE, in order to go back into Earths ancient history, and prevent dolphin and human kind from ever existing. This creates a paradox which fits in with the "Nibiru" theory, in that the Atlantians technology is SO advanced because it comes from somewhere else entirely; the highly advanced Vortex race.
So Ecco travels back into a hostile sea, where he must once again penetrate the Vortex Hive, to stop the Vortex from using the Time Machine. At the same time, he must ensure that the Time Machines technology is not wiped out.
The Atlantians use the time machine to escape into the past, to the time that was selected, and passed down through the ages. They discover that they have ended up in a hostile world, and before using their superior technology to destroy the somewhat sensitive Vortex Hive, Ecco appears and warns them not to destroy the Time Machine. They obliterate the Vortex, essentially acting as the "Creatures she could not rule", and forcing the Vortex Queen to disperse her genes into the sea, a last survival attempt, so that her replicators could continue to exist, even if the hive did not.
Ecco tells the Atlantians here all about the time machine, about the paradoxical effects of his journey, but is careful NOT to tell them about their own destruction. He leaves them with the unfinished time machine, and a sea of Vortex technology. They know to send Ecco back to this period in time when he meets the Atlantians for the first time. They know what time to travel back to themselves just before Atlantis is destroyed. And, by taking a sample of Ecco's genetic code, they ensure he will be born at the appointed time, so that he can begin his journey and NOT be sucked up by the storm.
After this, Ecco travels to the Asterite one last time, who teleports Ecco to the point JUST AFTER the vortex larva uses the time machine. Here, he is finally able to destroy the device, while ensuring that all of the paradoxes are in their proper place. From here, he goes home, and due to the powers embedded in his genetic code that the Asterite had given him, he triggers evolutionary effects in the bloodline, which guarantees that his great ancestor, Trellia, will go back in time to aid him later in the future.
So some of the new paradoxes are as follows:
The Vortex create the Time Machine, which is used for their eventual destruction. The Vortex Larva uses this same Time Machine to go back, in order to invent said time machine, and ultimately, merge with the rest of Earths creatures genetically.
The Atlantians go back into the past and essentially ensure that they will do so in the future, by leaving their predecessors hints and knowledge that will allow them to save themselves before their inevitable attack on the Vortex eventually wipes them out. They travel back in time, and thereby, ensure that later on, they will...travel back in time.
The Atlantians use Ecco's own genetic stock to ensure that Ecco will be born at the appointed time, so that he can save the world, etc.
Ecco destroys the time machine AFTER the paradoxes take place, and with his upgraded genetic material, acts as a trigger for dolphin evolution, which will allow Trellia to come back and help him later on.
I'm sure there are more, and I'm sure there are plenty of holes, or things I have left out. I plan to spend a great deal of time hammering out the details, etc, but I found it an interesting thing, to come up with as many convoluted paradoxes as possible, while attempting to tie the whole thing up some how.
Plus, Ecco finally gets that happy ending that was so well deserved
As for the "game" itself, it would follow standard Ecco formula, however the game would likely have more of a focus on action, much like Tides of Time. In the beginning there would be a lot of puzzles and story, but as soon as the Atlantians send Ecco back to take on the new Vortex Hive, it would be go time.
