If we believe that there is such a thing as Time Traveler's Immunity and Time Bastard we find ourselves with a sticky situation explaining how Marle can suffer from the Grandfather Paradox. I believe I have an answer. It's not an amazing one but it's still an idea. In this theory I'll allow the Entity to have decided what time period to have sent Marle back to (creating a situation which would set off a chain of events to save the planet) but I'll explain in a moment why I believe that the Pendant was the cause for the Telepod to transport her through time and not the Entity as some believe.
I can think of 5 ways a person can go backwards in time in Chrono Trigger.
1. Marle's Pendant. It sent Marle and Crono back in time.
2. The Gate Key. It's the device through which time travel is done for the most part of in the game until you get the Epoch.
3. The Epoch. Balthazar's creation that can go to any time period you have accessed.
4. A gate created by Lavos. Lavos transported people through time at the Ocean Palace and at Magus's Castle.
5. The Time Crash. Chronopolis was sent back in time but unlike other forms of time travel this affected a large 3 dimensional area and as pointed out in an article on this site, the area didn't travel but those 3 dimensional coordinates pointed to different time coordinates at the same 3 dimensional location.
Marle's time travel situation was actually different than Crono's. Crono traveled back in time with the Pendant whereas Marle was sent back because of it. Does that make any difference? I believe so. I believe that the five examples I just listed are different than what Marle experienced. I also believe that Time Traveler's Immunity doesn't just happen to you because you travel through time. I'll first explain why I don't believe Marle could experience a Grandfather Paradox because of any of the five examples I listed.
First off, the Time Crash. Going to Chronopolis would not send her backwards in time. Going there would send her to a place that really hasn't been sent back in time, just the coordinates for it point to a different time than it should be in (this is based on an article here on the Compendium). Marle cannot go back in time here and create a Grandfather Paradox.
Secondly, Gate Keys. I don't know how they really work or why, but they do. That said, anyone who uses them receives the Time Traveler's Immunity. If you use the Gate Key or are with someone that uses it then you won't experience the Grandfather Paradox. Time/nature has a way of balancing things out (like getting rid of extra copies of people for instance) which means that somehow it takes note of you when you travel through time. The Gate Key is a way for time/nature to take note of you. My reasoning for this is when you go to The End of Time there are portals there but after you use a gate more portals appear. You can be sent back through a portal you have been through which means that somehow time/nature keeps track of where you have been. Thus you are granted immunity from the effects of time travel. I also think the Gate Key might be made out of Dreamstone but there's no way of knowing. I'll get to why I think that it being made of Dreamstone would be important in a moment.
Thirdly, gates created by Lavos. They usually send people forwards in time, but when Lavos appears at Magus's Castle it sends Magus and the Chrono Crew back in time and apparently to different time periods. The Crew had a Gate Key so Magus might have been under the effect of traveling with the key. Magus may have been sent to the same time period as the others and woken up before they were found and taken to the village. Then again he may have been sent to a different time period and might not have been under the effect of the key. He changes his own history by appearing as The Prophet and having an effect (even minimal) to his past self. That would cause the future Janus to be different, thereby sending Magus to the Darkness Beyond Time. I think there's an answer to that too. Lavos seems to exist in a Pocket Dimension, kind of living outside the normal confines of time. Traveling through a gate that Lavos created would give one Time Traveler's Immunity. I'll explain why that would give you immunity in a moment as well.
Fourth up is the Epoch. Once again hell if I understand the mechanics of the machine, they're not explained in the game. Anyways, it's possible that the Epoch could send you to any time period you wanted but since that's beyond the ability of a game, you can only go to the time periods you've been to as well as the Day of Lavos. It makes more sense that the Epoch would be limited to its destinations in time because the Neo-Epoch seems to have the ability to go to any time, and an upgrade like that would make it worthy of the name Neo-Epoch. One additional way it would make sense that the Epoch is limited to the time periods you've been to would be if the Epoch could somehow determine where you have been (I think Star Trek: Voyager has talked about being able to read what time period someone's from) and then go there. Maybe there are special materials that go into making the Epoch (like maybe Dreamstone helps it travel through time). Does someone who uses the Epoch automatically receive Time Traveler's Immunity? I'm actually not sure. If the Epoch utilizes something like Dreamstone to help it travel through time, then I think so. We can't know this for sure since everyone who rides the Epoch has either used the Gate Key already or has been sent through time because of Lavos so we don't have a "pure" subject to test it on. I do think there's a good chance it would give you immunity because we see people from other time periods at the end of the game (explaining why they're there is a whole other topic, I personally think it's possible they were picked up before Lavos was beaten, giving them immunity to the effects of defeating Lavos, and therefore someone like Doan could go back in time to be at the fair).
The fifth and final thing is the Pendant. It is made out of Dreamstone, a special material used to create some of the most important items in the game: the Pendant, the Mammon Machine, and the Masamune. The Mammon Machine was created to commune with Lavos who doesn't interact with time normally. If Lavos does indeed exist inside a pocket dimension then Dreamstone must have some interesting temporal qualities. This is given more credibility when you think about how the whole adventure started. Marle, wearing the Pendant made of Dreamstone stepped inside a machine designed to relocate a person's spacial coordinates. The temporal qualities of the Pendant caused the machine to relocate Marle's temporal coordinates instead since she wound up in the same spacial location. The Entity, perhaps aware of what would happen, and having created gates for the heroes to use, decided what time period to send her to.
Now to tie everything together. I believe that traveling through a gate with an item with temporal qualities or travleing through a gate caused by something with temporal qualities grants one Time Traveler's Immunity. The Pendant is made of Dreamstone which appears to have temporal qualities since it can commune with Lavos who apparently exists in a Pocket Dimension. Crono had the Pendant with him when he went back in time and when the timeline was changed because of the disappearance of Marle's ancestor (which would have changed Crono's history and therefore changed Crono and would have sent him to the Dimension Beyond Time if the didn't have immunity) he wasn't affected. After Lucca created the Gate Key (which has apparent temporal qualities because it can manipulate gates but might possibly be made of Dreamstone) anyone who traveled with them never had to worry about disappearing because of their actions in the past. Lavos has temporal qualities and created a gate which sent Magus into the past. The Epoch might have temporal qualities since it can travel through time on its own without the need of a gate. It apparently just needs to know the time periods the people piloting it have been to in order to know what time periods it can go to. I also think it makes sense if Dreamstone somehow powered that time travel mechanism, but there's no way to know that.
That leaves us with Marle who was sent back in time because of the Pendant but did not travel with it. She is the one case in which someone went backwards in time and was not with something with temporal qualities or was sent back by Lavos who has temporal qualities. She's also the only person to experience the Grandfather Paradox.
Two quick things of note: Even though we changed the events in Zeal it still had the same outcome. In the original history it makes sense that Frog would have found the missing queen at the Cathedral anyways. Frog would have found a way to have conquered Magus in the original timeline because we are told he was defeated. We helped Ayla but the dinosaurs in the past still would have died out after Lavos hit the Earth. Simply put: events still had the same results after we went back in time. I don't think the creators of the game expected us to believe that going back in time and trying to change things that ended with the same result as before would cause the original timeline to be sent to the Darkness Beyond Time because a few protons and electrons are out of place because of our presence.
Also I think it's pretty interesting to note that all time travel done without a Gate Key (assuming it's not made of Dreamstone) or futuristic technology (the Epoch and whatever was used in the Time Crash) was done in the presence of Dreamstone. The Pendant at the beginning, Mammon Machine at the Ocean Palace, and the Masamune at Magus's Castle.
Sorry it's such a long post, let me know if you can think of anything that might confirm or contradict my ideas.
