The following have been deduced from Terranigma (or 天地創造), my favorite SNES game, and I believe, the best game to start with if you need to learn a foreign language by deducing it.
I think he is saying something about being able to use your magic by looking into the items room and equipping jewels.
Okay, I do not know the hiragana equivalent of some of the words I am seeing, but I can probably recognize the word and its meaning the next time I see it. The words in yellow refers to a room in this box for your items. The symbols before the の is referring to the items room, and I can only imagine the symbols after are referring to some sort of section, room or chamber, because it always appears in all four sections of the rooms that hold your various items.
The two characters on the middle line two characters from the last ones suggest to me it refers to jewelry, since I recognize the last symbol looks like it means stone or something.
(I believe he is saying that this is some sort of bookshelf.)
The last words in yellow after の I think is a bookshelf. The last symbol is probably the word for a book.
"This is the mirror of strength."
つよさ - this is probably a mirror. And the symbol after the の is most likely the word for strength, as it was in the game in English and German.
"This is the map."
The words in yellow mean (land) map.
If I'm not mistaken, the symbol on the bottom line after the space is to read.
EDIT: I found the corresponding symbol for it. It's 読む. More vocabulary from high school.
"On to the next room..."
The first symbol probably means next.
"Items you have received go in this room. Use and equip items with the X button."
The first few words, which literally mean to have in your hand (I think?) is idiomatic for things that you have received. There are more examples of those later. I am unsure about the verb here, the first symbol on the middle line, as it is a very common verb, and could be anything. I'll watch and wait. 使う - to use; another word from my high school days. And the two symbols near the end means to equip, or something similar. There are better examples of this later as well.
Has something to do with getting the explanation of an item which is the item above (I presume they are referring to the currently selected item) with the L button.
The last two symbols just before the last character before the space on the first line probably mean explanation.
"This is the weapons room."
The first two yellow symbols probably means weapons.
"This is the armor room."
And I think the first yellow symbols means armor.
"Alright. Go to the weapons room again."
もう一度 - more literally once more; but typically used to mean again.
行く - to go
"Ark received a weapon!"
So here is another example of "hold in the hand"; used idiomatically to mean you received something. Not sure why one of the kanji symbols is missing though. The context seems to me to be the same though.
I think he's saying something to the effect of hearing something, and to return outside the box.
The first character on the bottom line probably means box or container, and the one after the の next to it means outside. もどろう I believe means to return.
"I don't understand. Ark...I...I'm scared. Whatever it is, I'm still scared..." (At least that's what I think it says.)
こわい, also saw it as こわっ I think means to be afraid.
"Therefore...please...don't leave me alone..."
The last line literally means to be by one person (ひとり, also used in the context of 1 player, as in a 1 player game); it's most likely an idiomatic expression for being alone.
"Ooh, scary! But everyone in this village right now is already (take your pick; they're doomed, or they're all just like Elle. Not sure which at this point.)"
The symbol between the two の on the second line means village.
"Hey! What's the meaning of this? Are you running away?" (Not sure what the second to last sentence is but...)
The second line I hear a lot in English subs of some animes, and it often occurs when characters are asking about what's going on in confusion. The last one I also hear a lot in Bleach English subs; にげる - to run away, escape
"Of course! The elder! He can tell me the cure, since that box belongs to the old man!" (something like that...)
そうだ - Of course; used as an interjection, kind of like Eureka!
The two symbols after the space on the first line probably mean the elder.
The first character of the second line is probably to cure. Could also be restore, recover, heal, etc. Something having to do with returning the village people back to normal.
じいさん - old man; also おじいさん
Something about asking the old man what he knows about this (the villagers all being petrified).
知って - to know
"Hey! What's the meaning of this!? Explain, old man!"
Another example where the first two characters on the last line means explanation.
I think the character after の on the first line is most likely the word for state or status.
"Do you want to restore the status of this village?"
(Or more idiomatically, do you want to restore the village?)
This is probably a better example than the last one.
He's basically telling Ark to leave the village and go outside where he will find five towers.
Another example of the symbol for outside being used on the second line. I believe 出 means to leave.
The last symbol in the yellow phrase on the bottom line means tower.
He says he has opened the gate and wonders if Ark will succeed in curing everyone. It's phrased more like will you save everyone?
門 - Gate; from "senkaimon" a special gate, which I hear often when characters in Bleach are referring to a specific gate.
開ける - to open
"This is the gate the old man was talking about..."
Another example for gate.
In the line where Yomi (that purple bat thing) is next to, I think it says to pick up and throw. I thought it interesting to mention, because the first character for throw also appears in the word for upload, which I saw on Pixiv.
A better example which shows that the first two symbols at the top (and the one being selected) means to equip.
ヤリ - spear
And conversely, you have unequip. Or its equivalent. It may even mean to strip or simply take off.
はずす - unequip; take off
"I am the watcher/guardian of the tower. What are you doing here?"
The characters after the space on the second line is the guardian of the tower. I guess that makes the symbol after の guard or protect, or something similar.
"Ark received magirock!"
Another example of that "hold in the hand" thing. I think that literally says "prime blue" in yellow, but in the English translation, they're magirock (and Kristall in German).