Phantasy Star: Fringes of Algo

Kind of off topic of the Sapphire but still relevant I think,

SEARREN'S OLD CAVE (after rescuing Lann(Thea))

Lyle:
Ayn! Words can't express my gratitude. Use the Twins' Ruby Lann(Thea) has!
Long ago, I used that ruby to sneak into Riik's(Landen) world...

Theory:
Lyle seriously had his work cut out for him, he never used the Layan temples to travel. He went from Aqua - Aridia - Landen but in dragon form he could fly so would of done it pretty quickly. Also being Layan he didn't have to worry too much about monsters. If you check the Landen map, the Island Cave would of been a good stop off or resting point for Lyle. Rhys could of caught Lyle just before he left the Island Cave. There was also no other way for Lena to get to Aqua so obviously Lyle took her against her will or willingly.

Rhys' Generation
Lyle:
The truth is, I wanted to travel along with you to see many different
things...
...such as the world...or you...
But, the fact is, I have to go do some things to help out my comrades...
Perhaps we'll meet again someplace...

Theory
Seems like Lyle already had Lena with him.

Ayn's Generation
Hazatak android:
- SOME PEOPLE WHO LOOKED LIKE LAIAN REFUGEES FLED TO THE WEST.
AMONG THEM WAS THE MAN WHO STOLE THE TWINS' RUBY FROM US TWENTY YEARS AGO AND FLED TO RIIK VIA THE NORTHWEST CAVE.

Conclusion:
Lyle definitely took the gem.

Theory:
While in Hazatak Lyle could of learnt about the weather control tower, Azura and Dalhia, the sand bridge to access Cille and the two gems necessary, when he found out Lena had the Moon Stone he took her with him.

I also think Lyle hated Orakians with every fibre of his being, only after he took Lena with him and journeyed with Rhys, that he started to change his views on Orakians, he saw that Orakians were no different than Layans, that what he was brought up to believe was false.

Man, what I wouldn't do to get my hands on the translated version of Nial's quest and the 3rd generation, the only way that seems possible is if I learn Japanese.

Sure Junkie, I'd be honored.

Is it every explained how the different passageway-opening jewels actually function? Is cave actually closed with a place to insert the jewel in order to make the door open? Does the jewel make a force field blocking the entrance disappear?

I don't think it was explained. The gems are referenced as being a "key" to the "sealed" passages, but the nature of the seal - door, force field, or otherwise - was never explained. Once the key is used, the passage remains open, however. One of the guys in Lashute references that.

I always thought of it as some kind of slot with a door because of the key reference.

That's how I pictured it too - like there was a slot in a door that the gems fit into.