Chrono Cross/WMG

Serge is the reincarnation of Magus, aka Janus, from the first game in the series, Chrono Trigger.
It's implied that most of the cast from Trigger died. "Radical Dreamers," a Japanese-only game which became a prototype of Chrono Cross, directly states that "Gil" is Magus, but this angle was dropped and "Gil" became the character "Guile." Yet in a letter written to Kid, the reincarnation/daughter/clone of his sister Schala, it says that he is close by and protecting her and that they have to find each other. Kid and Serge can't be together because the Reset Button in the Good Ending erased Serge's memories of her and she'd be intruding; but Kid's next reincarnation is shown looking for Janus. Very reminiscent of "A Chinese Ghost Story."
 * I hope not. The movie at the end of the game shows Serge and Kid in a wedding photo.
 * Reincarnation makes previous lives genetics a non-issue.
 * Strangely enough despite the game claiming Serge would lose all memory of the events of the game, when you are transported back to the beach with Leena, Serge clearly remembers everything that had transpired. Either this loss of memory was meant for everyone except him and Kid or this was quite an oversight by Square.
 * I interpreted him asking about FATE and Terra Tower when Leena asked him if he was alright from fainting as the "echoes" of the memories; quickly being forgotten like a dream.
 * Except Guile is already Magus. After beating the Bonus Boss in the DS re-release of Trigger, Magus shows up, says he's going off to find his sister, and jumps through the distortion. Word of God confirms that Guile was always intended to be Magus; it'd just be too convoluted to explain his backstory on top of all the other weirdness that goes on.

Serge and Guile are both Magus
At the end of the Bonus Dungeon in Chrono Trigger, we see that regardless of whether your party killed Magus or not at the Road Cone; a Magus from a different timeline is still alive. If you survive the Dream Devourer, this Magus refuses to leave and gets his memory erased by Schala and presumably becomes Guile. The Magus who was killed by the Masamune was reincarnated into Serge but due to the connection of having been previously killed by the combined power of Lavos and Zeal (the Masamune) he has a link to Schala.
 * But why would Lucca write the letter if Magus Prime was killed in her timeline?

Miguel is Crono, or at least one universe's version of him.
While the spirits of Crono, Marle, and Lucca appear frequently throughout the game, it is said that these are "echoes" of a timeline which no longer exists. This has lead many fans to speculate as to exactly what happened to Crono himself. Proponents of this idea have several pieces of (admittedly circumstantial) evidence. Miguel's red hair, the name of his daughter (Leena, as a possible reference to Leene), his absent wife, his position in relation to the Crono-spirit (it always stands near/over him), his status as possibly the most difficult boss in the game, his knowledge of the future, his approximate age, and several ambiguous lines of dialogue are all cited as evidence. It is believed that he may have changed his name and moved to Serge's home after the fall of Guardia, possibly so that Leena could be brought up in peace.
 * Not only the hardest boss, but (as I recall) one of only three white innates. Which matches Crono's Light power-set.
 * Alternatively, Crono and Marle were killed in the fall of Guardia, and entrusted the safety of their daughter Leena to their close friend and bodyguard Miguel, who fled to distant Arni Village. Leena was so young when this happened that she assumes her true father is Miguel, who never had the chance to tell her the truth.
 * At the very least Leena has to be their daughter. She looks like Marle and has Chrono's red hair. I can't believe that's a coincidence.

Harle is the other world version of Kid
Ignoring the makeup, they are similar looking, and neither character is shown to have a counterpart in the opposite world. This troper also recalls a fortune that was the same for both of them, but cannot Google it; no doubt another troper will correct this reference.
 * Interestingly enough, this is only partially true. There's only one Harle, but there is two of Kid. Word of God puts Kid(H) up on the Zenan mainland.
 * And Harle(H) was frozen in the Dead Sea alongside the Home World Dragoons and Lynx(H), so, Jossed.
 * The fact there are two Harles (one in the Dead Sea) and two Kids (one on the Zenan mainland) does not preclude Harle still being Kid's physical/soul double, either through Schala's own actions (her corruption by Lavos creating a self to "destroy what she loves so much") or the Dragon Gods using her body as a template. It just means that like everyone else, Harle and Kid were split when Serge's dying/being saved created the alternate dimension. The original source of all the physical, soul, and fortune similarities would still be the fact they were both daughter-clones of Schala, it's just that instead of being Kid's Evil Twin (a literal biological counterpart), Harle would be her Evil Counterpart (a metaphorical one created by the Dragon Gods or Schala herself to combat Kid's actions). Then they both got split by the dimensional distortion.
 * "In your eyes, I perceive...both the look of a beauty and the look of a beast. Be mindful not to bring about your own end, my dear! A dream lies in wait, reaching out to engulf you!" Same thing for both. I checked.
 * To be fair, both are spot on for what are stated to be different reasons. Harle is the Moon Dragon, whereas Kid is created after the merge with Lavos. Which could probably spawn another WMG legion in of itself.
 * Plus, they both have the same Catch Phrase (That they are gonna kick your butt/derriere to the moons.)
 * They are both daughter-clones of Schala. The reason you don't see Harle's height and weight is that they would be identical to Kid's. Harle was a clone created by the Dragons to unseal FATE and let them take over the planet, while Kid was created to save Serge's life when he nearly drowned.
 * That isn't inconsistent with being counterparts, since counterparts would have similar origins.
 * To clarify, Kid is Schala's Daughter-Clone created to save Serge. Harle then, is made by the Time Devourer (Lavos) through the Dragon God to essentially prevent itself from being deleted. The Dragon God failed to defeat Serge in accordance to the Time Devourer's Will though, and Harle dies. Strangely both Kid and Harle has similar fortunes...except for one key difference. Kid has an opmistic future while Harle has a crushing fate instead.
 * It could also be that Harle isn't DIRECTLY related to Kid, but perhaps due to Harle being  she chose the only human form she had access to in order to reach Serge. Since   it was the easiest template to gain access to.

Magus is not present in Chrono Cross because he discovered a new threat to the planet
This explains why he was AWOL when Serge and Co. were trying to save Schala. Admittedly, it is hard to think of a threat more serious than a being that can devour all time and space. Maybe he discovered the source of Lavos and figured out there's more beings like it.
 * That's not news, it's spelled out in CT that the apocalypse is part of Lavos' reproductive cycle; it arrives from the sky, feeds on the planet for millions of years, destroys it and spawns baby Lavos to shoot off into space and find other planets. There's likely no single source, and even if there was, Magus would be unlikely to care about the well-being of other planets so long as his sister is still an issue.

Schala is the real villain.
Think about it. The DS port just established that she so hated humanity that she made it nearly impossible for them to rescue her and thus save themselves and really, life itself. Chrono Cross is entirely her fault. Her only method given created war and torment for millions and had Belthazar not been a better Chessmaster than her, any one of the steps taken could have wiped out life on Earth. Of all the people in history she could have saved, people in the throes of suffering, she plucked out a kid she fancied. And after the credits, she's stalking him again after resetting his memories. Nobody has been saved - all you did was give her the freedom to start all over again.
 * I've read it as her pacifism being extremely perverted by Fusion Dance with Lavos. Lavos wants to use her powers to stay alive, but has to distort her philosophy in order to do so. Likewise, Schala/Lavos sends the means to stop themselves to Kid and Serge.
 * The Chriosphinx also had a demented "How dare you use violence to prevent me from killing you!" mentality.

The cast of Chrono Trigger didn't die.
They grabbed a couple of those dolls they used to replace Chrono the first time to fake their own deaths. Now they are hiding somewhen in the time stream. Though frankly I don't get what implied that they died in the first place.
 * Lucca- the orphanage she ran was burned to the ground, and most of the children killed. If she survived, no way she would have let Lynx get away.
 * She could have been captured by Lynx and holed up in Chronopolis. Lynx wanted her to undo the Prometheus lock and in order to do that he would need to take her to Chronopolis alive; he would have nothing to gain from killing her outright.
 * Crono and Marle- Guardina is mentioned to have fallen to the Porre army. A kingdom generally isn't considered as being fallen if the queen and prince consort are still alive, especially if between them they can revive the recently dead, control lightning strikes en masse and cause massive Wrath of God type explosions with it, and cause localized ice ages.
 * This is based solely on assumption. Nothing is explicitly stated about their deaths.
 * Robo- reduced to a program deleted during the course of the game
 * Computer programs can be copied and modified without destroying the original. I doubt Lucca would put Robo in mortal danger without some kind of backup plan.
 * The rest died of natural causes during their respective eras, except Magus, who was in the game in amnesiac form as Guile.


 * If we do assume that the cast of Chrono Trigger didn't die, then it's even more bizarre that they sit back and do nothing while Porre subjectifies the rest of the world to their rule and horrible time-monsters are wandering around.
 * They should probably know that they're in an altered Bad Future that will be retconned away once Balthazar's Unwitting Pawn does his stuff, unless Balthazar was actually so incredibly dickish as to not give them a head's up. They're probably just lying low trying to stay alive until history resets to its no-FATE-Elements-or-El-Nido state upon the Devourer's undoing and and not messing with Porre or events in El Nido for fear of what might happen if persons of their power- and understanding of events- get mind-whammied by the emotion-and-memory-altering Records of FATE.


 * Well, there is pretty much no way Lynx or Dalton could take any of the cast on in a fair fight. But maybe they just showed the original cast in another world? And throughout the game's events they're having adventures while trying to get back home and fix everything.

The cast of Chrono Trigger are alive after Chrono Cross
Porre defeating Guardia was "allowed" because the Guru of Time was working with the Chrono Trigger cast to set up the circumstances to create the Chrono Cross. Ironically, since the Time Devourer was outside time and the result of paradox already; once it's been removed then all the changes to the timeline required to fight it no longer occurred without so much as a time hiccup. FATE no longer exists because it was created to combat the Time Devourer, likewise the Porre army being technologically advanced wasn't needed either. The Dragons no longer exist because they were shunted into this timeline to balance Chronopolis and FATE. Dalton does show up in Guardia, but gets his butt kicked again.

Schala had to do some editing in order to make the post-Time Devourer timeline
Most of the El Nido islands were only there because of Chronopolis and the Dragons. Despite the reset, she didn't want Serge and company to not exist, so had to manipulate things so that the islands and the cast still came into being.
 * Alternatively, after the Chronopolis Research Institute made El Nido for company housing (or something like it) after not vanishing in 2400, Serge and company were born naturally and raised in their proper era of The Future (since they were, technically, time-displaced in the Devourer-affected timeline), and all the El Nido characters are simply researchers, support staff, and families, plus workers of the inevitable related and unrelated industries that sprout up in company towns that size. Kid still exists because of the Power Girl Effect, falling through the cracks unaltered and unerased as the timeline repairs itself. The ending was sufficiently vague as to obfuscate the fact that its taking place in 12400 rather than 1020.

Guile isn't Magus or a brand new character...he's Magus's cat Alfador.
] At some point after Chrono Trigger, Alfador ended up in the 1000s AD (maybe he snuck on board the Epoch while the party was doing other stuff). While searching for Janus/Magus (who lost his memory in the new ending of the DS version), he encountered the magician Sneff, who can turn humans into cats and back again. Sneff turned Alfador into a human, who adopted the name Guile and continued the search for his master. Further reasoning behind Guile being Alfador:


 * Guile's name in the Japanese version is Alf
 * Guile has purple hair, Alfador has purple fur
 * His element color is black, appropriate for someone whose master's alignment is Shadow
 * The fortune teller lady is extremely surprised to see what he looks like under his mask - maybe he's hiding some feline features?
 * Having originated from the kingdom of Zeal, Alfador may have absorbed some of Zeal's ambient magical power, explaining his magical abilities in human form

Chrono Cross' plot was sabotaged.
The game's original plot would have placed Chrono Cross as an actual sequel to Chrono Trigger. However, an executive, who was a Final Fantasy fanatic, feared that the game would fare better than the upcoming Final Fantasy IX, and managed to get his hands on the script so he could modify the narrative pacing and some other plot elements, so Chrono Cross's status as a sequel to Trigger would actually be contested, and FFIX would have a better reputation solely because of the plot.
 * Uh, except for the fact that Chrono Cross is most definitely a sequel. Yes, you could eliminate all references to Trigger and have a game that stands on its own...but if you preserve those references, the entire game makes sense. Serge's very existence threatens to undo everything the Trigger cast slaved for - Another World, where Serge dies, is the canonical world (Keystone T-1) that Trigger plays out in. Serge's survival, as explained by Balthasar, causes Home World to fission off. Because of the nature of the Time Devourer, if it is allowed to exist in any timeline, it will mature and devour everything. Not to mention which, FF IX was kind of dumb anyway, so this theoretical conspiracy falls flat.

The C&Ds of the fangames are a case of Creator Backlash.
Square has come to hate the Chrono series ever since the Magus-Guile issue. Which would explain perfectly the C&Ds on Chrono Resurrection and Crimson Echoes, and why Chrono Break will never be developed - they will not allow the games they so revile to be continued or expanded upon, even in fanon.

The Devs think that you should be dead.
The Mind Screw Gainax Ending of the game suggests that there is a Schala Kid-clone out there looking for you, in the real world. Now, this sort of thing happens to Serge because he dies in his 'correct timeline,' so the Magical Girl Schala sends her daughter-clone into the past to save him. But that doesn't change the fact that, without her interference, he should be dead. The ending sequence in the game depict a girl like Kid wandering around, who according to Word of God, is supposed to be looking for the audience, the player. Does that mean that Square wants us all dead, but we're only alive because of a fictional character's interference? Or in some other metaphysical sense, because of SQUARE's interference?

Fargo was an Acacia Dragoon.
He had a falling out with Viper after the latter supported Porre in their war with Guardia. Fargo either thought they should have supported Guardia instead or just stayed out of the conflict altogether, which led him to leave the dragoons and become a pirate. He might have even met Zelbess right after that, bitter about his homeland being dragged into a war that had nothing to do with them, and on what he saw was the wrong side, to boot. Remember Nikki's song, when you were restoring Marbule? It's a dramatic re-enactment of what happened to Fargo after he left.
 * It would explain why his daughter is a dragoon deva despite still being a kid (family connections and all), as well as Another!Fargo's surprising degree of honor for a bloodthirsty pirate. Being an ex-knight will do that to you.

Serge's great-great-great-etc. grandfather on his dad's side was Tata from Chrono Trigger.
Character art of Tata looks quite a bit like Serge (and like his father when we see what he looked like ) if you account for the differences in their art styles, and we already know that in this game world people from 600 AD can look ridiculously similar to their modern descendants even though there are hundreds of years between them.

Maybe when Tata grew up he couldn't stand the shame of everybody in his town knowing about that time he let everyone think he was a hero when he never ended up doing a heroic thing in his life, or maybe one of his kids or grandkids got tired of the Fake Ultimate Hero in their family being a bit of a town historical joke, and ended up wandering away to settle in the little out of the way archipelago where their family remained from then on. Or maybe one of his descendants just liked tropical locations and decided to move there. Either way, eventually Serge is born and he unknowingly more makes up for his forefather's lies by being a true hero.

Demi-humans are of mixed human and fiend ancestry.
Since the events of Chrono Trigger (specifically, the side quest to defeat Ozzie, Flea, and Slash) result in fiends (or Mystics, for those who insist on using the SNES version's translation) and humans being on good terms in the present day, it's possible that in the new good future established by the defeat of Lavos, there are fiends employed at Chronopolis. When Chronopolis is sent back in the Time Crash and FATE has its inhabitants populate the newly-created El Nido, some of the fiends interbreed with humans. After many generations, pure-blood fiends are mostly bred out and demi-humans become their own distinct race.

Lynx becoming involved with Porre was all part of FATE's design.
Now obviously Lynx wouldn't do anything without FATE's directive, so let me be more specific as to my meaning. FATE's original prime directive was to make sure that no one in El Nido interfered with the Zenan mainland, so as to prevent the events of Chrono Trigger from being accidentally undone. To that end, when Porre rose as a great power and overthrew Guardia, FATE had Lynx join General Viper as a master strategist under the supposed auspices of keeping Porre out of El Nido, all while secretly being The Mole who also worked for Porre. The idea was to play both nations against each other, since this would keep people (like Viper and the Dragoons) too busy to go looking for the Frozen Flame and cause a change in the timestream at Chronopolis by mistake (or just interfere with her ability to direct events, as happened when Wazuki and Miguel's mission ended up severing her link to the Flame).

At the same time, however, because this occurred after Lynx's failed (or successful) attempt at drowning Serge, FATE had realized that because her mission was compromised without the Flame, it didn't really matter at that point if El Nido interfered with Zenan. What was more imperative was getting the link to the Flame back. So she directed Lynx to join both Porre and Viper Manor so as to give him access to two different sets of armies--in Home, as a means to break through the barrier around the Dead Sea/Sea of Eden; in Another, to coerce Serge (once he contacted a Record of Fate and revealed he was still alive) into helping him, or use the Dragon Tear upon him. (Her making use of a Dragonian artifact like that was likely an attempt at subverting the Dragon Gods' plans with a Spanner in the Works, but instead made her an Unwitting Pawn to both the gods and Belthasar.) Once the Flame was hers again, she would then either have had Lynx betray Viper so that El Nido fell to Porre (as it did anyway in Home after the dragoons' disappearance), or crush Porre, whichever would preserve the future timeline better.

As to why Lynx of Home World led the dragoons (and Harle) into the Dead Sea...firstly, to try and break down that barrier so he could get back to the Flame, but also to eliminate the dragoons so that El Nido would fall to Porre, as FATE had planned all along (to keep El Nido from interfering with the timeline). Harle getting caught in what happened was either a lucky break for FATE, or if she somehow had figured out Harle's real allegiance without her catching on (which she might have, since she knew the Dragon Gods were trying to break free of her), a clever way to also ruin the Dragon Gods' plans. Lynx getting caught in it too just made the plan an accidental Thanatos Gambit.