Yes, it's Princess, not Queen, and makes more sense this way. While the Queen's whereabouts may be unknown, the Princess (Marle) actually, literally, *vanished*. Sorry if I confused anyone by having it wrong for so long. In my defense, 王女 resembles both 女王 and 王妃, which both mean roughly "queen". More recently, I amended "The Vanished Princess" to "The Princess who Vanished" for parallelism with the last chapter ("The Queen who Returned").

At first glance, it looks just like an ordinary small chapel, with ordinary nuns. The holy-sounding, for lack of better words, 1-15 マノリア修道院 (Manoria Abbey) plays. And then Crono spots something on the floor.

Lucca: Did you find something?
A hair ornament...?
This's the Guardia royal
family's coat of arms!

The nuns surround Lucca and Crono. Shedding their disguises and attacking, they are revealed to be half-snake monsters. Lucca fights with a gun, but pulls out a hammer to hit with when at close range. Her stats are similar to Marle's, but with a bit more magic less speed. With tech points, she learns two techniques (one of which combos with Crono), then stops learning more, just like Crono and Marle. Her status screen has a red 火 (Fire) in the top corner, and much as Crono and Marle do for their respective elements, she has about a 1/5 innate resistance to fire attacks. Anyway, they beat up the monsters.

Another one suddenly appears and takes a swing at Lucca. 1-23 危機一髪 (Critical Moment) plays, but only very breifly, since right after Lucca screams....

...a froggish humanoid creature drops in and smites the foul demon with his broadsword. 1-20 ファンファーレ１ (Fanfare 1) plays. The newcomer wears simple armor, blue gloves and boots, and a forest green cape. And he's green and hops.

"Don't let your guard down to the very end.
It's when you're drunk with victory
that your defense is wide open.
Did you come to aid the Queen too?
It looks like it's their den from here on.
Okay, how about we go together?

Allow me to express my disdain for the NA version rendition of the frog's speech. There's no reason to have him use Elizabethan English, since he speaks normally (a bit coarsely, even) in the JP version, and it's a horribly mangled mockery of real Elizabethan English most of the time anyway. For example, "Will thee accompany me?" should be "Wilt thou accompany me?" if he's speaking to only one of them, and I believe it should be "Will you accompany me?" or "Will ye accompany me?" if he's speaking to both. "Thou" is a subject, "thee" is a direct object, "thy" and "thine" are possesive, and all of them are singular. It's too much work to point out all the errors, but I might mention the more disgusting ones....

Lucca: Y, you're...!?
Crono, you know, right?
I can't stand frogs...!

"Well, as long as I'm like this I guess it'd
be pointless telling you to trust me....
Fine, do what you want.
But I've got to help the Queen out....

Lucca: H, hold on....
You don't seem like a bad
fro... person....
Umm....
What'll we do, Crono?

Crono decides to work with the frog person. After all, he's skilled, familiar with the time period, and has the same goal.

Or else Crono gets stuck in another dialog loop until giving in. I'll stop mentioning these since they're fairly common and unimportant.

Lucca: L... let's put up with it,
and go together!
What's your name?

Naming time again. And the default happens to be....

Lucca: Yes, well then....
Don't be too hard on me, Frog.

Frog: Sure. I'm positive there ought to be a
secret passage somewhere in this room.
I'll bet we can get in the back from there.

There's an odd looking organ in the corner. Crono plays around with it, resulting in 1-16 道行く者へ祈りを… (Prayer to One Who Walks the Road...) and a secret door opening in the rear wall. In the secret section, 1-17 沈黙の光 (Silent Light) plays. Of course, there are monsters all over. Besides using a broadsword, Frog has techniques of his own, and can combo with Crono on one of them. Like the others, he stops learning skills after his second. His status screen has a blue 水 (Water) in the top corner, like Marle's, and he similarly has a small innate resistance to water. His stats are similar to Crono's, though he's not as fast. Fighting their way past the monsters, the party reaches a large chamber, where Critical Moment plays....

"Are you prepared, Queen Leene?
It's time to say goodbye to this world.

They rush into the room to see the queen being confronted by... the kingdom's chancellor...?

Chancellor: Oh? You...!!
Good job managing to slip in this far.

Frog: Your majesty, please step back!
We will take care of this one.

Chancellor: Gya, ha, ha...! Give it up!
I won't let a single one of you
leave here alive!
Hah! Worthless frog...!
I'll make a bloodbath of you all!
Chancellor....
Change!
YAKRA!! Ta-da!!

Right after yelling "change", he turns into a big yellow slimy monster. It's the first boss battle! Except for certain special ones, boss battles use 1-18 ボス・バトル１ (Boss Battle 1). Yakra strikes back at the whole party when attacked, but not when too close to the attacker. He also has a strong single-target needle attack. Of course, the party emerges victorious, otherwise it would be a very short game. Fanfare 1 plays until the party returns to the castle.

Leene: I knew you would come for me.
Thank you, Frog....

Frog: The king is worried about you.
Let us return to the castle.
Thanks for your help, Crono, Lucca.

Leene: Thank you very much.
Please come to the castle along
with us as well.

Before leaving, the party checks the treasure chests in the back. Inside one of them, oddly enough, is the....

Real Chancellor: Phew, I'm saved!
That damn monster, shutting
me up in a place like that...!
Oh, the Queen!?
The real me is here, as you can see.
I am perfectly lively!

Leene: Yes.
Then let us return to the castle.

No music as the scene begins.

Chancellor: That Yakra bastard.
Replacing me, kidnapping
Leene-sama, and all that....
Our Guardia Kingdom must
build a courthouse and prison
to strictly judge that sort!

Frog steps forward. 1-19 カエルのテーマ (Frog's Theme) plays.

Frog: Unable to protect Leene-sama
to the end, I have lost all honor.

Quick lesson in classical English: The '-th' verb ending is only for third-person singular subjects, such as "he", "she", and "it". For example, "he looketh", "she cometh", "it falleth", and so on. "I hath" is simply wrong. Similarly, the '-lt' and '-st' endings are only for use with the second-person singular subject (thou). For example, "thou shalt", "thou hast", etc.

Frog briefly bows, but quickly leaves the throne room without saying another word. Courage and Pride resumes. Crono speaks to the king.

Leene: I thank you very much
indeed for saving me.
If you had come any later, what
might have become of me...?
By the way, where is the girl whom
they say was mistaken for me?

Lucca: That's right!
I'd completely forgotten
about Princess Marledia!
Hey, Crono!
Where did Marledia-sama vanish?
Maybe there....

Crono and Lucca rush up the tower to the queen's room. Sure enough, Marle reappears there, and in her normal clothes, even though she was wearing one of Leene's fancy dresses when she disappeared. 2-12 ファンファーレ２ (Fanfare 2) plays, followed by silence.

Marle: Crono!
I was so scared....
Knowing I'm in a cold place
even though I'm not conscious,
I wonder if dying feels like that?

Lucca: Princess Marledia-sama,
may you be in good spirits....

Marle: You came for me too!
Marledia...?
Huh!?
Looks like my cover's blown....
Sorry, Crono.
I didn't mean to trick you.

Distant Promise begins playing.

Marle: I am Marledia.
My father is King Guardia XXXIII....
But even I wanted to wander around
and look at the fair with a boy.
If you'd known I was a princess....
Crono, you wouldn't have seen the
festival with me, right?

The JP version's phrasing indicates that Marle considers the side of her that wandered the fair with Crono like a normal girl to be more important to who she is than being a princess. The NA version loses this nuance.

Marle: See?
And I like being called Marle
better than Princess!

Marle: That's just like you, Crono!
We're friends!

さすが (sasuga) essentially refers to someone living up to their (high) reputation or to someone's (high) expectations.

Marle: The real Queen is back
in one piece too, right?
Let's go home too, Crono!

Courage and Pride resumes. Back downstairs in the throne room....

The Japanese expression literally means "two melons".

Marle: If you don't get along well
well with the King, I'll get mad....
I guess I can't either.

When I first played the NA version, I though she meant Crono and Lucca had better get going along home. Looking at the JP version, it looks like she's actually saying that the King and Queen need to get along with each other, which makes more sense. There's a probable pun too; 怒る (okoru) is to get mad, but 起こる (okoru) is to happen. Since neither kanji is used, Marle could also be saying she can't happen if they don't get along.

The king and queen stare at her oddly.

Marle: Never mind, anyway, may
you live happily ever after!

(Talking to the Queen again)

(Talking to the King again)

As the party leaves, they find Frog standing outside the throne room. He turns as they enter. Frog's Theme plays.

Frog: The Queen was exposed to
danger because I was near....
I'm leaving the castle.

Frog: 'Twas a fault of mine, which
endangered the Queen.
I shall depart for good.

He spots Marle, and walks up to her for a closer look.

Frog: You do indeed greatly resemble
the Queen.

Frog: Indeed, your resemblance
to the Queen is uncanny.

Frog: Crono, your swordsmanship
has considerable promise.

"thou hast potential", not "you hath"... yeesh.

Frog, sticking with his decision, quickly leaves the castle. The music fades out.

Lucca: ....
You're not bad either, Frog.

With history back the way it was (sort of, more on that later), and Marle safe, the party heads back to hills where they arrived.

There's no portal visible here, but there is some sort of small pulsing dark blue sphere. Fanfare 1, which seems to double as Lucca's theme, plays.

Lucca: W, well then, Marle....
Please observe.

Lucca pulls out a strange key-like device. The sphere responds by opening into a portal, like the earlier ones.

Marle: Kyah!
Lucca, that's AWESOME!

Lucca: Ohohoho...!
Ah, excuse me...!

Marle: You can talk normally too!
You're more amazing than I am!
I might be a princess, but I can't
do a thing.

Lucca has, up to this point, been using the extremely respectful form of Japanese that is appropriate for speaking to people like princesses. Marle's apparently sick of this, and tells her to talk like she would to just anyone.

Lucca: Then I'll take you up on that....
I named this distortion a "Gate"....
A Gate is something like a "portal" that
links the same place in different eras.
As far as appearing and disappearing
goes, the Gate itself is unstable.
Accordingly, I applied the principles
of the Telepod, and use this....
Gate Holder to stabilize the Gate.

ゲート is just "gate" written phonetically in katakana. 門 is the kanji that means gate, portal, etc..

Marle: But why did this Gate appear
all of a sudden then?

Lucca: It could have been the Telepod's
effect, or possibly something else....

Marle: This's kinda complicated....
Anyhow, let's return to our era!

Lucca: Yeah, okay.
Let's go back, Crono!

They step into the Gate, it closes, and they pass through to the other side.