The Masamune is actually the Ruby Knife, a weapon created by Melchior to destroy the Mammon Machine in 12,000 BC. The reason it is so effective against Magus is because, as royalty from the 12,000 BC magic kingdom fueled by that power, his magic must have likewise originally come from the Mammon Machine. The Ruby Knife was also made of Dreamstone, the same stuff used to create the Mammon Machine. The Mammon Machine siphons magic from Lavos, so it wouldn't be surprising that the Masamune can also siphon energy.
Crono never ever died! He was just taken from the party so that the party in the future, both literally and storytelling-wise, could have him. All that got destroyed was a clone. You're not rewriting history by making a clone take the hit for Crono, you're keeping him alive, but letting your past selves believe he died!Maybe... If you believe it to be a Stable Time Loop.
Isn't this basically stated in-game?
I thought it was left to interpretation.
If you watch the Chrono-demolition scene carefully, there's a moment when his body flickers, as if he had changed position slightly in an instant... or been replaced by a clone.
Marle and Lucca travel in the Epoch to save Crono.
Crono and his friends are the exact kind of creatures Lavos was trying to cultivate and harvest; they're capable of punching out the universe's version of Cthulhu. Ayla serves as a testament to why humans were chosen for genetic modification.
Over the course of the game, the Masamune is revealed to be as powerful as one's belief and confidence is, right? Not just on a symbolic level, either: its power is shown to be directly proportional to the faith one wields it with. In that sense, the Masamune draws energy directly from the wielder. This makes perfect sense once you realize how the Masamune was created. I mean, it's only logical to assume that a weapon created from a power-siphoning machine would be a power-siphoner itself.
How did Marle end up with her pendant? The pendant that originally belonged to Schala? Simple: Schala gave the pendant to her little brother, Janus/Magus, who in the original timeline wound up in 600 A.D. The Kingdom of Guardia was at war with Magus, and won. The Guardia royal family came into possession of the pendant because it was part of the spoils, and it was passed down the family line.
Another possibility that could be considered Fridge Horror: It's stated that Marle is Ayla's descendant, and that the Zeal family is also Ayla's descendants. In order for this family to have that connection, someone from the Zeal family must have survived the fall of Zeal. But since Queen Zeal, Schala, and Janus' fates are all accounted for, there's only one real possibility: Schala had a kid at some point before Crono and co arrived, and that kid survived the fall of Zeal.
That... doesn't work. Not only is Marle not stated to descend from the Zeal family in your supposition, but Ayla lived 65'000'000 years ago. There probably isn't a human on the planet that's not descended from Ayla.
Besides which, the pendant and the amulet are seperate objects. At no point did Janus every have Schala's pendant. The Amulet is the metal object seen hanging from Magus's hip in official artwork.
It's actually rather simple. Schala lost the pendant when she was thrown into the Darkness Beyond Time, which survived the Ocean Palace's destruction, eventually washing up on land sometime in the several millennia between 12,000 BC and the Kingdom Of Guardia and picked up by someone, either one of Guardia line's descendants or some random person and it gets passed around until it ends up in the Guardia line's hands, and eventually ends up in Marle's possession.
Dinosaurs are weak to lightning. This makes no sense in the English version beyond giving them a type weakness, but a more accurate translation of the element from the original Japanese is Heavenly. So we have billion year old creatures being defeated by a religious concept. Someone at Square trying to make a subtle statement maybe?
Most likely a case of Nintendo's well known strict censorship policies.
More likely than that would be that the heavens, in the form of a meteor, are most likely responsible for wiping out the dinosaurs in real life, or Lavos, a virtual meteor, in-game.
If you visit Chrono's house after the Black Omen rises from the ocean, Chrono's mom will comment on "how beautiful it looks today." For everyone who lived after 12,000 BC, the black omen has basically been sitting there doing nothing, so why would anyone in other eras believe it was ominous? It would be like saying the Great Pyramid (and in this case, it's even older than that) was actually a doomsday machine controlled by an immortal being, after all these years.
In the animated opening of the game, we are shown a photo of the entire cast except Magus (to hide the fact he will become a playable character). So since all the other characters are in the photo, who took it? While it's possible it was Crono's mom, or Taban or Lara, a hilarious and heartwarming possibility is that it was Magus. On the one hand, it shows he really does care about them; on the other hand, just try and imagine his expression and tone as he is pressed into service and asks them to say cheese or some such!
Even with Nintendo's censorship policies, a lot of explicitly religious themes still shine through. Leaving aside Ted Woolsey's brilliant naming of the Three Gurus after the (traditional) Three Wise Men, there's the ominously-named Mammon Machine, and the way that Zeal's architecture is practically littered with graven images that smack of fertility idols and demonic pagan deities. Anyone who knows a bit of Christian theology, an archaic term or two from the King James Bible, and some of the popular mythology about lost prehistoric kingdoms such as Atlantis should pretty easily be able to guess there's something seriously wrong with the Kingdom of Zeal even before learning its people are getting their power from Lavos, the evil time-warping planet-consuming Eldritch Abomination whose name is all too reminiscent of a Fire and Brimstone Hell. Zeal is a hard-core heathen empire; and as such, its doom is practically a Foregone Conclusion.
Azala knew about Lavos, and her words after her defeat imply that the ice age is a direct result of her defeat. She displays telekinetic abilities in battle, so it's not a stretch that Azala had been in psychic contact with Lavos and was aware that it was deciding which of the two terran races it was going to use for its harvests. Azala was hunting the humans because her race's survival depended on it.
The first time you fight Lavos in 12,000 BC, it is absurdly strong compared to future encounters. Schala weakened it by destroying it from the inside out when it tried to incorporate her, but even then, it was STILL able to destroy the world in 1999.
Sending Magus back to 12,000 BC was a Batman Gambit. Lavos knew that Magus would try to save Schala in the Ocean Palace, and would have succeeded if Crono's party hadn't intervened. Magus was almost indirectly responsible for the destruction of the world.
Due to your stumbling around the time stream, Marle briefly vanishes from existence. When she returns after you Set Right What Once Went Wrong, she tells Crono that her absence was "awful" and she was "somewhere cold, dark... and lonely." In other words, she was aware even when Ret Gone. Consider now all the additional alterations you make to history throughout the game, which you don't correct later, and how likely it is that you erased thousands or even millions of people from history (you made changes in the age of dinosaurs!) Millions doomed to an isolated limbo before they were even born...
The ending gotten if the party defeats Lavos before defeating Azala, although comedic in tone, may upgrade this to an entire intelligent species. It's the exact same Good Morning, Crono and Millenial Fair sequence from the beginning of the game, except everyone is now a Reptite. Essentially, if Lavos did not crash into the Earth, the Reptites would have won the war, and almost certainly slaughtered Ayla and her people, along with the rest of the human race.
The Awful Truth as told by Lucca, Robo or Magus if they are brought along for the final battle. They mention that Lavos cultivates all of the lifeforms on the planet and then harvests their DNA, sending its offspring out into space to repeat the cycle. If that's the case, then Lavos may not have been the only one of its species to begin with. How many other planets have undergone or are currently undergoing the same fate, and what if this was the first time such a powerful entity was able to be stopped?
This only gets worse thanks to Chrono Cross; Lavos was brought back thanks to the power of Schala and time paradoxes to become the Time Devourer, and it's implied that it's fully sentient and aware of what Serge and friends are doing and pissed about it. Only a single one of these creatures nearly manages to end time itself by landing on Earth out of coincidence, through planning, some luck, and its own sheer power. And if there's a whole race of them out there...
In the original timeline, the humans defeated the Reptites. However, one of the alternate endings has the Reptites emerging victorious. The change came about because Azala originally did not create the Black Tyranno, until she saw the stolen Gate Key, assumed the humans had advanced far beyond the Reptites, and quickly created the Black Tyranno as a countermeasure!
As is evidenced by the first half of the game, the Black Omen didn't exist until Crono et al meddled with the timeline. Why not? Because in the unmodified timeline, Crono and his gang weren't there. In the timeline that was modified by Crono's presence, after he's disintegrated by Lavos, Schala uses the last of her power to teleport his friends out of the Ocean Palace. In the unmodified timeline, who would she have chosen to save instead? Herself and Queen Zeal. This is a terrifying concept for two reasons. Firstly, it makes Crono and his friends indirectly responsible for everything that subsequently happened to Schala. Secondly, how many other things about the past have Crono and his friends changed simply by being there?
No matter what you do, Lavos continues to exist! Chrono Cross existing is the more obvious proof, but there is another one which is easily missed. In the final battle against Lavos, there is a humanoid alien-ish creature and two bits, one for offense and one for healing. The healing one cannot ever be damaged and you only win the battle by destroying the big guy. Problem here is the healing bit's shadow remains visible when everything vanishes into light, proving you didn't really kill Lavos.
In the Lost Sanctum, one kind of enemy you can fight are called exiles. Exiles look like the normal, civilized, and anthropomorphic Reptites, so their minds work exactly the same way as humans. This means that the Reptites send members of their own kind to die in the wilderness.
Helped along slightly by the fact that being exiled is what kept them from being killed with the rest of their race.
The main ending mentions Robo's uncertain fate as he heads back to a version of 2300 in which the Day of Lavos never happened. This future's an unknown quantity, but it seems almost certain that he'll be 300 years obsolete, since we has built during or before 1999. (Though the save "Save Crono's Mom" ending shows him hanging out with Atropos, so I guess obsolete robots are permitted to continue?)
During the first trip to Prehistory, the Reptites steal the Gate Key, preventing the party from using the gates. However, the player can still switch party members. Since the reserve members are hanging out at The End of Time, how are they getting to the party (or, more importantly, how are the current party members getting back to The End of Time)?
Gameplay mechanic. The no-more-than-three rule is violated multiple times over the course of the game.
Simple solution: All the members of the party are actively traveling around with the main party. This even gives an explanation why they're always shunted to the end of time whenever they use a gate to travel. They're abusing the rules of the universe to create a safe haven in case they get in trouble, or if they're going somewhere they don't know is safe.
In the beginning, Marle fades from existence briefly because her appearance means that nobody ever rescues Leene. However, If Marle never existed, Crono wouldn't have bumped into her at the Millennial Fair, and the pendant would not have been there to open the first Gate. Therefore, Crono wouldn't have been thrown back in time, so he also should have been subject to the same Temporal Paradox that Marle was. How does Crono resist fading when Marle disappears?
Three words: Delayed Ripple Effect. Marle didn't disappear as soon as she was mistaken for the queen, so Crono didn't either. Marle, being a direct descendant of Queen Leene, happened to disappear faster.
This also applies to Magus, since Janus isn't in the room with the Mammon Machine when the party interferes with the past.