We know that once a person has time traveled, he or she is protected from his or her changes to history and always emerges at the point of arrival on the timeline (Time Traveler's Immunity). We also know that Lavos seemingly exists in a Pocket Dimension, as defeating the shell in 1999 A.D. makes the shell disappear in 12000 B.C. However, Lavos's behavior interferes with these principles. Chrono Trigger and Chrono Cross suggest that Lavos was defeated in 12000 B.C. when the party went to the Black Omen. This is evidenced by the Black Omen's need to be destroyed to fully complete the game and its inability to be destroyed in 1999 A.D. A Chronopolis quote also notes that no information can be gathered on Lavos in the current timeline as Crono and his friends prevented him from existing:
~~~~ -- LAVOS -- ~~~~ ~ ~~~~~~~~~~~~~~~ An extraterrestrial life-form that is thought to have fallen from the heavens 65 million years ago. On the time line that existed before history was changed, Lavos was assumed to have slept deep below the planet's surface... Sleeping and consuming the planet's energy up until the day of destruction known as the '"Apocalypse."' There are those who believe that, 12 thousand years ago, the legendary ancient magical civilization known as Zeal came into contact with Lavos. That fateful encounter is said to have resulted in Zeal disappearing from the surface of the planet within the space of a single night. However, the very existence of the ancient civilization of Zeal has never been proven, so up till this day this theory cannot be confirmed. On some time lines, Lavos appeared on the surface of the planet in the year 1999 and brought the world to ruins. However, a group of young time travelers saw where their planet's history was heading and, through their actions, rewrote time. This very research facility exists on that new time line... In a world where, thanks to the defeat of Lavos by the young adventurers, the Apocalypse never happened... On a temporal vector where human civilization continued to evolve unhampered. All the data on Lavos that was obtained from tracing different parallel world possibilities has proven to be volatile, with fluctuating discrepencies. Perhaps, at this point in time, it is nearly impossible to obtain any true information about Lavos.
Now, remember that in 2300 A.D., Crono observes Lavos coming out of the ground to destroy the world. This establishes that Lavos as having Time Traveler's Immunity, as exiting a Pocket Dimension would grant the creature that status. Since Zeal falls on all timelines after Chrono Trigger, we know this to be true (otherwise Lavos would not emerge from his Pocket Dimension and destroy Zeal at the Ocean Palace disaster after his defeat). With this in mind, consider what would happen even if Lavos were defeated in 12000 B.C. He would still erupt in 1999 A.D., as his existence there is protected by Time Traveler's Immunity! Lavos's actions are incongruent with the principles of time and dimensional travel; otherwise, the future would be destroyed regardless of the point of Lavos's defeat. Only if Lavos were defeated in 1999 A.D. would this be remedied, and we know that he was defeated in 12000 B.C. Are there any possible solutions for this problem?
This paradox is negated partially by Chronopolis, and partially by gameplay. Firstly, even if Lavos were defeated in 1999 A.D. after a failed eruption, Chronopolis would still be unable to glean any data from the resulting magmatic hole in the ground. Lavos predated Chronopolis and the fact that he's no longer in his Pocket Dimension would prevent the time research facility from obtaining any hard evidence of Lavos, short of time traveling to points like Magus's summoning or the eruption itself. And Belthasar is the only one who can do this in the future, as he alone has the Neo Epoch. Next, the handling of the game is also skewed and can invoke gameplay negation. If you complete the Black Omen in 12000 B.C., Lavos seems to erupt from the ocean. But if you lose to Lavos at this point, the ending scene in 1999 A.D. plays with Lavos already erupted in that era! Due to the way the game handles the myriad ways you can approach the Lavos fight and the "game over" ending, it's tenuous to try and pass off these actions as canon. In this case, Chrono Cross can simply establish what actually happened, and in this case, Lavos's defeat can still canonically occur in 1999 A.D. without error or Pocket Dimension negation. If further justification is needed, one can assume that the party defeated the Black Omen and retreated to face Lavos in 1999 A.D., or that they entered Lavos's Pocket Dimension at the time of his eruption.
One can simply suppose that Lavos exited his Pocket Dimension in 1999 A.D. or dissolved it at that point. We know that the Pocket Dimension theory is sound because Lavos does not change in strength no matter what era he's faced via the Black Omen; players still fight the same Lavos. Granted, that's a gameplay corollary, but this is a problem of gameplay regardless. One may think that if one believes Lavos has really been around for sixty five million years, the 0.02% of that time the heroes can face him wouldn't make much of a difference in his strength. However, that 0.02% of time witnessed the birth of human civilization and knowledge, whose intelligence (and use of magic in Zeal) would provide him with much better DNA than millions of years of plants ever would. It would stand to reason that Lavos gained more strength in the human period than in the millions of years of apes.
Originally, this was listed as a plot hole before truth regarding Chronopolis became evident. The following Gameplay Negation of Pocket Dimensions attempted to explain the occurrence.
The framework could work if the rule of Pocket Dimensions granting Time Traveler's Immunity were negated. Lavos's destroying Zeal would still be preserved since he is defeated after the event, and he would not be guaranteed emergence in 1999 A.D. Nonetheless, this causes a number of problems. Firstly, it hampers the notion of Time Error, which is clearly demonstrated by the End of Time. Secondly, it is known that time traveling to the End of Time is a protected act, as Gaspar remains there even though canned by the Prophet in the Keystone Timelines. If one argues that Lavos simply didn't have a Pocket Dimension, the problem of his shell comes into play. Which leads us to the supposition that this paradox is simply a result of gameplay mechanics. The developers did not plan to force the player to defeat the shell twice, and Lavos's shell only utilizes one location within the game's data -- meaning regardless of where it is defeated, it will remain that way if accessed again. With this gameplay excuse, one can make a case for Lavos's not having a Pocket Dimension at the cost of the plot inconsistency of his shell. In any case, an attractive solution is impossible.
From: Common Questions