Using Lucca's Time Egg, the Masamune lends you some of its power and sends you back in time to save Kid.
The prisoner in Terra Tower says that the seal of FATE on the Dragons has broken, and humanity can be considered Lavos's offspring as Lavos interfered with human evolution after contact with the Frozen Flame.
[Prisoner]
When I was still human, I was locked up here, and I have been here ever since...
This tower is a fortress belonging to the ancient Reptites... A symbol of revenge, brought against mankind by the Dragons...
With the defeat of FATE, the seal has been broken and this tower has surfaced...
In the eyes of the Dragons, we humans are the foes...
A brain that has developed abnormally to 3 times the original size in the span of 3 million years...
We humans have evolved at an enormous rate because of our contact with Lavos's flame...
In a sense, mankind is Lavos's offspring...
We humans are extraneous to this planet...
The prisoner is a great being made of stone.
The Prophet (who surprise surprise, was Belthasar all along), meets you in a space which is not a space (and looks like Vipor Manor).
[Prophet]
This is a space that does not exist. But don't mind that... More importantly, I have something I must explain to you!
Lavos created the dimensional vortex which threw Belthasar into the far future.
[Belthasar]
Well, that was up until the Queen of Zeal attempted to harness the power of Lavos... Let's just say, things got out of control and Lavos created a dimensional vortex that threw me far into the future!
In the far future, Belthasar combined his knowledge of magic and the advanced technology to make huge progress in time research (which lead to the creation of Chronopolis and the Time Crash).
[Belthasar]
There, I seized the opportunity to study the science of the future... I was then able to apply to that the knowledge I brought from my own era, including magic, which was long lost in the future. Anyway, this led me to make huge progress in the research of time.
Well, that research led to the creation of Chronopolis and to the Time Crash... You might think I really blew it, but perhaps it was really my finest hour! Ho-ho-hoh...
Belthasar created a compact time machine called the Neo Epoch and used it to follow Chronopolis and Fate to the past.
[Belthasar]
Anyway... I created a compact time machine that I dubbed the '"Neo Epoch."' I used it to time warp to this age to learn of Chronopolis and FATE's plans, and to see how things were turning out.
Terra Tower/Dinopolis was pulled from another dimensions future to counter Chronopolis being pulled into the past by Lavos. Chronopolis wins and Terra Tower was sealed away.
[Belthasar]
Terra Tower is really a city of the Reptites, from another dimension's future...
It was originally '"Dinopolis"'... The castle of Azala's descendants, who achieved an evolution much more intimate with our planet.
Dinopolis was drawn into this dimension's past about ten thousand years ago...
This was done so that it would serve as a counter-balance against Chronopolis, which Lavos pulled here.
Needless to say, a fierce battle ensued...
In the end, Chronopolis emerged as the victor, and the Reptite's fortress was sealed away by FATE...
We actually see the battle between Chronopolis and Dinopolis. Jets battle pterodactyl-like creatures and fireballs rain from the sky.
FATE sealed away the Dragon Gods powers, and became a god itself. The Dragon Gods used Serge and the others in order to destroy FATE and be free (with the Dragon Gods being in opposition to humanity while FATE was humanities protector).
[Belthasar]
But then FATE sealed away the Dragon Gods' powers, in effect becoming a god itself. Thus the islands where the new godhead, FATE, existed came to be called the Sea of Eden instead.
Perhaps you didn't realize it, but you were used by the Dragon Gods to eliminate FATE!
It was not true that the Dragon Gods sealed away the Frozen Flame... Rather, it's quite the opposite... It was FATE that used the power of the Flame to seal up the Dragon Gods. In reality, the Dragon Gods are in opposition to man, while FATE itself was actually the protector of humanity!
The Dragon Gods were originally a single plasma life form, and a living accumulation of the planets energy (with their dragon-like forms being "pseudo-guises" so they can appear in this dimension). It served as a biological machine to control the natural energy of the planet for the future Reptites, but FATE divided the Dragon God up and scattered and sealed them. After FATEs defeat, the seven Dragon Gods crossed dimensions and merged back into the one Dragon God
[Belthasar]
The Dragon Gods were originally a singular plasma life-form... ...A living accumulation of the planet's energy! Originally it was a biological machine used to control the powers of nature in the future society of the Reptites. In order to control the natural energy itself, FATE divided the one Dragon God entity up into 6 weaker plasma life-forms... Then scattered them across the land and sealed them away. Their dragon-like appearances are just pseudo-guises... ...Temporary forms they take so that they can appear in this dimension.
But all that changed when FATE was vanquished and its powerhold was eliminated! At that moment, the seven Dragons who had been rendered almost powerless and forgotten... traveled across the dimensions to reunite into a single entity!
Originally there were six Dragons, but a seventh was created by the others to help break FATEs hold. Due to the Time Crash, a new moon has appeared in the skies (which is why there's only one moon in Chrono Trigger but two in Chrono Cross). The seven main celestial bodies in the skies correspond to a different dragon, with Yellow, Green, Black, Red & Blue corresponding to the five stars, the White Dragon corresponding to the larger moon, and the smaller moon corresponding to the Dark Moon Dragon. This final dragon is actually Harle (this would further show that the Dragons aren't bound to a single planet).
Belthasar:
There were six Dragons you knew of and one more hidden Dragon you didn't... Like the second moon that once was lost, but later was found... Although the same planet, my world didn't have two moons! Look up at the night sky now and you will see seven celestial bodies... Five stars and two moons... Five brother stars that correspond to the five colored Dragons, ruling like gods over the night skies... One moon that corresponds to the white Sky Dragon... And another darker, daughter moon to counterbalance them.
The Fire Dragon, the Water Dragon, the Green Dragon, the Earth Dragon, the Black Dragon, the Sky Dragon, and one more... The final Dragon... The dark moon Dragon... The one who was to work to free the other Dragons from their bondage by the FATE computer... The child the others created on the night of the electric storm that temporarily caused FATE to loosen its hold on them...
I believe you knew her as... Harle.
The Chrono Cross has the power to transfer memories and cross space and time, and can combine all the melodies of the world.
[Crono?]
Hey, mister! Is that the Chrono Cross you guys have there? What? You guys don't have the Chrono Cross? The Chrono Cross... The melody and harmony... It has the power to cross space and time and unify people's thoughts and feelings... It has the power to transfer memories... By using it as an Element, it has the power to draw on the sounds of the six colored Elements to produce a healing harmony... It has the power to combine the sounds of the world into one melody...
Belthasar finishes by saying he's sure he'll meet you again in one time period or another.
[Belthasar]
I'm sure we'll meet again soon, in one time period or another... Be careful now... And good luck...!