The party wakes up in a small room that looks fairly sophisticated. There's a door in the front side of the room, and a ladder in the back. It's impossible to switch party members here, or even to rearrange the order of the characters who are already in the party!

Since your party is fixed for a long time from when you talk to the elder in the town square, it was a pain compiling all the different comments everyone can make... interesting, maybe... but it's one thing that motivated me to switch to text dumps as my main source of lines. :-P

Incidentally, I strongly recommend having Ayla in your party for this part, preferably not as the lead character.

Nice try, and the grammar's even correct for once, but "evanesced" doesn't apply here, unless the equipment faded away like mist clearing.

Ayla: That "money" stuff you can
trade for anything gone too.

Aren't Ayla's lines supposed to have no particles and lots of spaces? Well, whatever.

Ayla: Ayla can fight!
Get everyone weapons back!
Beat that guy!

The party tries the door first. It's locked, of course, and there's a guard outside.

Guard: Serves you right. Bet you can't
do a thing without your weapons.

So they try the ladder. It goes to a small ledge outside, where the wind howls, and clouds are visible some distance below.

It's an arms-flailing, catching-his-balance sort of noise.

Frog: Th-the sky!
Then, this is...

The screen pans across a large jet aircraft.

Lucca: !?
There's an air duct.

Robo: PLEASE wait!
It seems to BE an air duct.

Frog: Mh!?
We can go up from here...

Ayla: !!
Wind coming in here too.

Lucca: I get it.
We'll lure the guard in.

Robo: I SEE, we will induce
the guard to be careless.

The pun isn't anywhere near as bad in Japanese. It's probably a stretch to say it's there at all.

Frog: I get it, you mean
to lure the guard in.

Ayla: Ayla healthy...!
If {char1} say so, then fine.

The character playing sick acts sick and cries out.

Frog: It hurts!
M-my navel HURTS!

Robo: M-malfunction!
Control offline! P-PLEASE help!

Ayla: Graaah!
Ayla huuurt!

The guard foolishly rushes into the room, where the character playing sick promptly knocks him out.

Frog: Heh, moron.
As if frogs have navels!

Ayla: ......
Ayla hate lie...

That's enough to get out of the room, but they get thrown right back in if caught (unless Ayla is in the party... she can fight back, while the guards are so weak that having no armor hardly matters), and the sick ploy won't work again.

So they take to the vents... It's easy enough to hop up into the ventilation system, and there's plenty of room to move around.

Lucca: We can sound out the situation
inside the plane from here.

Frog: We can see what the enemy's
up to from there...

Robo: We CAN look in there to
grasp the enemy's disposition.

Most vents show nothing of particular interest, but one reveals a chest by a sleeping guard. The party can sneak in and take back the lead character's equipment from the chest (which is why Ayla shouldn't be in the lead). Once anyone is armed (or Ayla is in the party, as she always counts as being armed), guards have to fight the party instead of simply throwing them back into captivity. However, only armed characters can fight or gain experience and tech points. Don't worry; the guards are pathetically weak.

The Dalton Corps (Basher) guards have a measly 150 hit points each, no remarkable attacks, and normal defenses. In some locations, the robotic Byte adds to the security. It's a bit tougher and takes about half typical damage from physical attacks, but shouldn't pose any more of a threat than the guards.

I never understood how removing their weapons suddenly makes everyone but Ayla helpless. Marle and Lucca are powerful mages, Frog also has magic and should know a thing or two about fighting unarmed anyway, and Robo has his lasers and other built-in weaponry on top of exceptional strength and one heck of a bodyslam. All of them should be quite capable of fighting unarmed or even (if shame allows) buck naked. Presumably it's just an excuse to make the sneaking part matter, and to avoid the trouble of making weaponless combat sprites. That, and feeling powerless seems to be something of a theme of this part of the game, especially after how well the whole Abyssal Temple incident went.

A chest guarded by two guards (outside) and a robot sentry (inside) holds the second character's equipment, one with two guards has the third character's equipment, the money is in a chest with three guards, and two guards and a robot sentry guard the items. It doesn't hurt for the party to go ahead and take out every guard on the plane as long as they're here anyway, since nowhere else do such laughable foes give so many experience and tech points.

If you get the items before everyone has their equipment back, you can pass out any spares you have, allowing anyone so outfitted to fight normally. Getting back the equipment they were using when captured re-equips that and returns the spares to the inventory. Also, retrieving the items lets the party find a Magic Capsule in the vents, in a dead end that appears to be empty as long as the items are missing.

Speaking of the vents, there's an interesting one at one end of the ship...

No, the party hasn't been spotted. Through the vent they see Dalton overseeing and yelling at some lackeys, who are doing something to the Sylbird.

Lucca: H-hey!
That guy's tampering with the Sylbird!

Frog: That lowlife, how dare he
meddle with other people's stuff!

Robo: It seems he IS modifying
the Sylbird.

"Strange Happening" plays. Dalton resumes yelling at his underlings.

Dalton: No slacking off!
After all, this is the great new
king Dalton's flying throne!
Now the world will have to
do my bidding.
Hyaah hah haa!

One of the doors in the plane leads out onto the wing.

Lucca: Hold on! We still haven't gotten
everything back yet, okay!?

Robo: There ARE other things that
were taken; IS that acceptable?

Frog: There's still stuff we haven't gotten
back. Are you okay with that?

Ayla: There still taken stuff!
Okay anyway?

The winds on the wing blow the party toward the tail of the aircraft. There are turret enemies here that, like the rocks on Grief Mountain, lock all techniques and items, are hard to hit, and leave combat if not killed fairly quickly, but give 100 tech points each if taken out.

Each Site (Turret) has somewhat more health and evasion than a Rokk, and they also shoot lasers, but as before, Ayla with an accessory to raise hit rate is your best bet. Also try to avoid encountering more than one at a time, since it's much harder to kill two before they run than it is to take out just one.

Robo: This IS a powerful magic energy
reaction!

A portal opens, and yet another golem comes out, though this one is a somewhat different color.

Boss battle time. At least that's what the music indicates. The Master Golem (Golem Boss) actually talks...

The Master Golem counts down from five to one, doing nothing else. Then...

The Master Golem again counts down from five to one, doing nothing else. Then...

The Master Golem curls up and looks very nervous.

For what it's worth, the Master Golem speaks in a feminine style.

After a little longer, the Master Golem runs away, without so much as attacking once. Alternately, inflicting enough damage quickly enough can kill it for experience, tech points, and money. However, there's nothing to steal from it.

The Master Golem has a lot of health, but all its defenses are normal. Use your strongest attacks, regardless of type, if you're going for the kill.

Meanwhile...

: Hu ha ha...
It's done! It's done!!

The scene fades into to show Dalton perched in the Sylbird, which now has wings. "Strange Happening" plays.

Dalton: Behold these beautiful wings!
THIS is the great new king Dalton's throne.
I name it...

DALTON: See these beautiful wings!
Now THIS is a King's throne.
I now name it...

Dalton: The Sky Dalton Throne!
And now, its first sacrifices will be them!

DALTON: The Aero-Dalton Imperial!
And THEY'RE gonna be my first
victims!

Dalton: Lift off!
Sky Dalton Throne!!

"Chrono Trigger" starts playing. Dalton gets annoyed.

Dalton: Wrong, all wrong!
Stop the music!

"Stop the music" is in Japanized English, in case you were wondering.

The music cuts off, and switches to "Critical Moment".

Dalton: Hu ha ha! Yes, this is it!
Launching!

A bay door opens in front of him.

Dalton: Sky Dalton Throne!
LIFTOFF!

The Sky Dal... err, Sylbird, leaves the bay, knocking the flunkies over in the backdraft. The music stops, and the scene switches back to the wing as the Sylbird streaks by.

"Critical Moment" starts up again.

Dalton: It's not the Sylbird!
It's the Sky Dalton Throne!!

DALTON: It's not {Epoch}!
It's the Aero-Dalton Imperial!

Dalton: Hya hya hyaaah!!
This time, I swear, I'm done with you all!

DALTON: Mwa, ha, haha!!
You are excess baggage!

DALTON: Make like the wind and blow
outta here...!

Dalton twists the idiom 海のもくず (umi no mokuzu, scraps of seaweed in the ocean), which refers to dying at sea.

Dalton hits a button, and the Sylbird fires lasers that narrowly miss hitting the party.

Dalton: Hya ha ha!
Squirming like worms!

Frog: Dammit!
Such arrogance!

Marle: It's you guys' fault...!
Crono...
GIVE BACK CRONO!!

The character who spoke leaps onto the Sylbird, followed by the others. "Boss Battle 1" plays.

Dalton R (Dalton Plus) has a few new tricks, otherwise it would be boring, right? The only one of note is that he strikes back when hit with elemental attacks...

Also, he uses his annoying halve-target-hit-points attack when hit with non-elemental or Aether attacks.

Apparently Dalton just doesn't have what it takes to handle the Dark element. Though possibly the AI scripter didn't realize anyone could have a Aether attack without Crono (Robo's final technique is the only one possible with the characters available), so coded specific counters for Fire, Ice, and Dark, while leaving the 1/2 HP attack as an "everything else" case.

Since he's still Dalton, he still doesn't have many hit points, and when he runs out, he tries summoning...

...but just gets sucked into his own portal and vanishes without a trace.

Robo: MORE importantly, if we do not know
how to pilot it, we WILL keep falling...

Everyone gets into the ship to check it out, and "Critical Moment" starts up yet again.

Robo: I HAVE never dealt with this
type of meter...

The lead character hits the button—press Y—and the lasers activate, striking the wing of the Blackbird.

The lead character hits the button—press X—which seems to restart the engines. Meanwhile, the heavily damaged Blackbird gets worse and falls faster... Elsewhere, in the town square, the people see this and rejoice.

The internal storyline progression tracking variable is now 0xD2.

Scene change back to the Sylbird. 3-10 シルバード～時を渡る翼～ (Sylbird ~Wings that Cross Time~) plays, as it normally does when the party flies the Sylbird, now that it flies.

Robo: I should HAVE made a direct
connection to MY unit.

Frog: This feels great!
Though I guess I've got to admit
it's thanks to that lowlife.

Ayla: Sylbird healthy!
Sylbird became bird!!

Robo: This is what IS called
a lucky break, is it NOT?
Though unexpectedly, we HAVE
obtained flight capabilities!

Missing the point entirely...

Lucca: And here I'd been thinking
about modifying it myself...

Lucca: !!
Our items were here!

Robo: !!
THESE are OUR items!

Ayla: !!
Aylas's stuff here!!

And someone else adds...

And someone else adds...

Frog here correctly uses the seaweed idiom that Dalton twisted earlier.

Robo: The Sylbird WAS safe.
Surely, Crono too...

Ayla: Cro strong!
Cro not die!!

The party flies the Sylbird back to the village, landing in the outskirts.

Marle: Crono's gotta be somewhere!
I'm looking for him!!

Lucca: Maybe Crono's managed to
make it to this island too...

Frog: Guess we'll try searching for Crono,
never mind whether he's dead or alive...

Ayla: Search Crono!
Crono alive for sure!!

Ayla's forgetting to use the "Cro" nickname again.

After taking out some Anger on Dalton, we seem to have slid back into the Denial stage of grief.

There are more people here than before. Jyaki's cat Alphard has turned up too, and is following a little boy around. There's no sign of Jyaki, though, or Sara, and of course Crono isn't here either, for that matter. Let's try asking around.

Elder: Everyone in the village is
gradually cheering up too...
We just have to start over...
That's all there is to it.

There's no sign of anyone (and no music), but something sparkles on the ground. The party investigates, and the Magus appears out of nowhere.

Everyone draws their weapons. The Magus ignores them.

Magus: Behold.
It's all at the bottom of the ocean...
Zeal, the eternal kingdom of dreams...

{Magus}: Behold.
Everything's at the bottom of the
sea.
Gone is the magical kingdom of Zeal,
and all the dreams and ambitions of
its people.

Magus: I lived there, once upon a time.
Though I wasn't who I am now...

{Magus}: I once lived there...
But I was another person then.

The internal storyline progression tracking variable is now 0xD3, starting the next chapter.

The following line found in the game data fits here, but appears to be unused.

The Magus has a flashback after this...

Knowing the prophet's identity and seeing the Magus's upcoming flashback tell us that some of the specifics of the events in this era have been altered. However, the overall outcome has not changed, and the devastation Lavos caused should be more than enough to wipe out any lasting effects of the divergence. So it looks as though, once again, the overall historical impact has been insignificant.

However, the issue of the prophet shows that defeating the Magus did have an effect that was not immediately obvious. Interrupting his summoning caused him to be thrown here, rather than whatever happened originally. My guess would be that his summoning worked well enough for him to get himself killed challenging Lavos, and to give the Demons enough of a glimpse of this powerful creature that they continued worshiping it and the Magus for centuries. However, the loss of their leader, even if he did seem to leave most of the day-to-day operations to Vinnegar, crippled their ability to wage war, and Guardia declared victory. Something similar happened in the modified timeline, but with the summoning disrupted, they didn't get their glimpse of Lavos to cement their reverence for the Magus, so Vinnegar and his heirs were able to seize the glory for themselves, and the descendants seem to have forgotten about Lavos entirely.

Anyway, while the party's intervention led to the Magus appearing here and claiming the mantle of prophet, that ultimately has no lasting historical effects.