I was thinking about "The Returned Queen", but that doesn't sound quite right...

Though you can't actually save just yet, the chapter switches over at the end of the scene in which Marle vanishes. I'll continue to split the sections accordingly.

Lucca: H-hey, Crono!
You're the one that brought her here!
Where do you think you're going!?

Lucca: Crono!
You brought her here, YOU get her
back!

So Crono, constrained by the plot, wanting to do something, probably feeling responsible, and again being more bold than sensible, picks up the pendant and heads for the Telepad... Crono's heroic theme, 1-2 クロノ・トリガー (Chrono Trigger) plays.

The alternate ending "The Dream Project" is no longer available after this, since the shortcut to the final boss won't be accessible for a while.

In an interesting bit of attention to detail, Marle's Pendant is returned to your inventory at this point.

Taban: Oh!
So, you're going after her, Crono.
Way to be a man!

Lucca: That's it!
We don't know what's beyond that space,
but it looks like there's no other way.

Taban: But we can't be sure the hole
will just conveniently appear again.

Big change in meaning. In the JP version, he's questioning whether they can get the distortion to appear at all. The problem of what might happen to anyone who goes through it hasn't even come up yet.

Lucca: It's worth trying!
The pendant has to be the key!
Crono!
Hold on to it tight, and the same
thing should happen for sure!

Lucca is being optimistic in the JP version. The NA version make it sound more like she's desperate and panicking.

Lucca: Engage energy charge!
Raise the output more!!

It's fairly obvious what this line means in context, but it's taken me longer to confirm it and figure out why. It turns out that 「あいさ」 is shortened from the English-derived 「アイアイサー」 ("aye aye, sir"). And on a side note, Wikipedia tells me that "aye aye, sir" indicates that an order has been heard, understood, and will be carried out promptly, as opposed to a plain "yes, sir" indicating simple agreement with a statement.

On yet another side note, "roger" doesn't really apply here, though it's been misused enough popularly that the intended meaning ought to be understood regardless. Procedural words like "roger" are normally used in radio communications, not in person. It's not the best choice for meaning, either, since "roger" indicates only that a transmission has been received and understood—the approrpiate response when intending to follow a received order is "wilco" (will comply).

The machine begins to spark, just like before.

Lucca: Bingo!!
It looks like it's working!!

As expected, space distorts and Crono is thrown into the middle of it.

Lucca: Once I investigate the cause,
I'll follow after you too!
I'm counting on you, Crono!

The rift closes, sending Crono on a brief trip through the distortion. Another rift on the other side opens into...

Crono lands in a clearing on a hillside. Several Jarry (Blue Imp) attack him as he tries to leave, but they're quite weak. After the battle, ambient sounds of nature replace the music. Fighting some more Jarry and an optional Ballmadillo (Roly), Crono leaves the hills to find himself on the edge of a village that strongly resembles his own. 1-9 風の憧憬 (Longing of the Wind) plays. The village is a bit too small to be Truce, and the hills are where Leene Plaza should be. Hoping to get his bearings, Crono tries talking to one of the villagers.

400 years in the past? That explains why the village is both so familiar and so different.

On a side note, the world map now says "A.D. 600" instead of "?". And now that that's established, I'll note that "Longing of the Wind" always plays on the A.D. 600 world map, rather than saying so every time.

Crono finds the town's pub in the same place as in the Modern Age, and checks inside for more information. Two soldiers are deep in conversation.

As they're talking, someone with strange and travel-worn clothes walks in and sits down. Crono tries talking to him.

Toma: You're not from here either?
I'm Toma the explorer.
If you treat me to a drink,
I'll give you some good info.
How 'bout it?

TOMA: Are you a stranger here, too?
I'm Toma, the explorer.
If you're buying, I'll tell you a story.
How about it?

Crono decides to humor him, at least for now. Any unusual news could help him find Marle.

Toma: Thanks for that. Now...
About how lady Leene went
missing...
I think that abbey they say was
built to the west is suspicious.
Huh? You say Queen Leene was
already found in the back hills?
Hmm... is that so...

TOMA: Thanks!
It's about the missing Queen.
She disappeared while visiting that
cathedral to the west, and...
Beg your pardon?
WHAT!?
They found her?
Never mind...

Since the only lead he's had is the queen's mysterious reappearance, Crono tries going to the castle. On the way, he must pass through Guardia Forest, which contains some slightly stronger monsters—Ballmadill Rider (Roly Rider), Cockadoodle (Blue Eaglet), and a different Jarry (Green Imp)—but still none worth particular notice. Don't miss the Power Capsule and the bush hiding a monster that runs away and drops a Shelter when disturbed.

The free Shetler is available every time you visit the forest, so feel free to stock up.

The castle is right where it is in Crono's time. The interior is stone, sparsely decorated with suits of armor and royal purple carpets. 1-13 ガルディア城～勇気と誇り～ (Guardia Castle ~Courage and Pride~) plays. Two soldiers stop Crono immediately upon his arrival.

SOLDIER: Halt!
Who goes there!

Soldier: I've never seen this guy.
And what's with that getup?
Could he work for the Magus's army?

SOLDIER: Check out that hair!
Where're you from, son?
Are you one of Magus's troopers?

Soldier: I really doubt such a wuss
would be with the Magus's army.

SOLDIER: Hardly! This kid never would
have made the cut!
Show us your stamp collection, son!

Soldier: Go on, get lost!
Stick around here too long
and we'll lock you up!

SOLDIER: Har, har!
Now beat it, shrimp!

The queen approaches. She has long blong hair and looks quite young, and oddly familiar...

Queen: That person is one to whom I am indebted.
Make him welcome, as a guest.

QUEEN: Show your manners!
This is a friend of mine!

SOLDIER: But there's something odd
about him!

Soldier: Surely not!
Feel free to pass!

SOLDIER: Forgive me, my lady!
Please enter, Sir!

Giggle? Anyway, she walks back where she came from. Crono is understandably confused. How could she even know him, much less be in his debt?

The internal storyline progression tracking variable is now 0x0F.

Regardless, in the throne room, the king wishes to speak with Crono.

King: Ah, it's you.
The one Leene is indebted to.
I offer my heartfelt thanks!
But what happened out there?
Leene hasn't been quite her usual self.
She even seems to have lost the coral
headdress she always wore.
And she treasured it so much...
Oh, pardon me.
I shall tell the Knight Captain about you.
Rest in the Knights' room in the left basement.

KING: Sir!
I understand that you are the one
who saved my dear wife, the Queen!
But can you tell me what happened?
Leene's acting rather odd.
And she seems to have lost her coral
pin, which is something she guarded
with her life...
Forgive me! You must be tired.
We can talk about this later.
Please rest in the Knights quarters,
downstairs, to the left.

Aside from talk about the ongoing war and the incident with the queen, many of the soldiers speak of a man universally respected who went missing years before.

On the other side of the castle are a dining hall and kitchen, where aside from seeing that the knight captain and head cook, who happen to be brothers, don't get along, we can also hear about more about the queen not being her usual self.

Eventually, Crono goes all the way up the right tower to see the queen. An elite guard meets him at the door.

Two handmaidens attend to the queen in her room, one with another interesting tidbit.

Anyway, on to the queen.

QUEEN: Ah!
There you are.

She turns to the attendants.

Queen: Please remove yourselves.
I would speak with this person.

QUEEN: Please leave us.
I need to talk to this individual.

The servants leave Crono and the queen alone together. The music fades out.

She turns around for a moment and stifles a giggle.

Queen: Just kidding! You came for me,
Crono!

It's clear what's going on now, right? 3-9 クロノとマール～遠い約束～ (Crono and Marle ~Distant Promise~), which sounds like a music box, plays.

Marle: Right, it's me!
Everyone calls me "Leene" for some reason.
But I'm glad.
Even though we were only together for just a
little while at the festival, you came for me.
Crono...
Thank you...

Marle: It's me!
But everyone calls me, Leene!
I'm so relieved you're here!
We barely know each other,
but somehow, I knew you'd come for
me...
Thank you, Crono!

The music fades out. Crono doesn't notice anything strange, but Marle...

Marle: Wh-what!?
!!
Wh-what IS this?
It's like my mind's going to pieces...

Marle: S, something's wrong!!!
W, what's happening?!
It feels like...I'm being torn apart!

It gets worse. She starts to look increasingly odd, like she's fading out of reality or something.

Marle: I-I'm scared!
It's like I'm going to disappear...
H-help me, Cro...

Marle: Help me, Crono!
I'm scared!!!
Please... Crono
...h, help me!

Crono moves as though to save her, but he doesn't even know what's happening, much less how to stop it. She vanishes without a trace, not even a rift in space-time as explanation.

The internal storyline progression tracking variable is now 0x10, starting the next chapter.

There's an intriguing analysis on The Game Design Forum of the design decisions that had to have gone into Chrono Trigger. Aside from evaluating things like the balance of exploration verses dungeon crawling, the function of NPCs in the game, the purpose of various battles in teaching the player gameplay skills, and other such things, one of their major points involves the historical impact the party's actions have. More specifically, the utter lack of any meaningful impact until late in the game, despite liberal application of time travel. So, I thought it might be interesting to go section by section and analyze the net effect the party's actions have had by the end of each chapter.

Here, we've only just discovered time travel and have already managed to break history. Right? Maybe not. While it's probably simply a case of different writers working on different parts of the story, the way time travel works in the CT universe rules out the Grandfather Paradox (which, as explained at the beginning of the next chapter, this basically is) by invoking something called time traveler's immunity. The basic idea is that as a time traveler, any changes you make to history do not directly affect you; my understanding is that in essence, even though the timeline has been changed, you still originate from the timeline you came from and answer only to that. So disrupting the search for Queen Leene cannot cause Marle to disappear, since she's from a timeline where the search was never interrupted. And as we find out in the next chapter, there's still a dedicated and skilled fighter looking for the queen, so it's quite possible that she's going to be found regardless. Furthermore, if there's still time—if Leene is still alive—would anything have changed yet anyway? And if she doesn't survive, why doesn't that change stop Crono and especially Lucca from following Marle back in time? If Marle was never born, then Crono never met her, she never tried out Lucca's teleporter, the pendant never reacted with it, and no one went back in time, so they have no one to follow, no reason to go to the past, and don't even know that it's possible!

So why does Marle disappear? Again, it's probably just a case of different writers, but the Chrono Compendium has an interesting theory that makes it work in-universe. In an optional event much later, the party theorizes that there is an "entity" that has guided Crono and the others in their travels, showing them things they need to know if they are to avert the disaster that becomes the central point of the game. Marle's disappearance may have been brought about by that entity as something of an object lesson about being careful about their actions, or even just to ensure that they get involved in a search that leads to some relevant information and at least one important meeting. Their belief that they significantly changed history also turns out to be a key part of prompting them to make the attempt at averting the larger disaster later on. If nothing dramatic had happened during this visit to the past, would that have left them with the impression that history is immutable and stopped the main quest before it even started? It's possible. Regardless, this theory is backed up by the fact that Marle vaguely remembers being somewhere—cold and not entirely conscious, but apparently not non-existent—when she returns. The entity stuck her somewhere other to motivate the group as a whole, then brought her back once the point was made, incidentally giving the illusion of significance to their actions.

Anyway, back to the point. While Marle's appearance has disrupted the search for the missing queen, and it appears as though this will lead to the queen's death and prevent Marle from ever being born, it's just as possible that the party's net historical impact so far has actually been negligible.