While the others install the helm (which takes a little time and effort, but is not particularly difficult [i.e. no skill check required]), Icarus and Zoide check out the other chambers on this deck. The second chamber is much like the first, while the third is an entirely empty spherical space, the only feature being a number of glyphs carved or scorched into the surface of the rock. [If you're searching thoroughly, make an Investigation check.]

Icarus Investigation 7

In the second chamber, Zoide finds a small metal canister that hasn't completely rusted away; inside it you find a spell scroll of Mold Earth.

[Does anyone have anything else they want to do before we skip forward in time a little?]

(I'm good skipping along)

Skippy skip

Da'Kal stretches her arms and dusts her hands waiting for what happens next.

It has been almost two and a half hours since Princess took her place at the helm and launched the Tyrant ship toward the edges of Realmspace at spelljamming speed, and the seas of Toril lie ten million miles behind you. While the rest of you relax on the command deck [everyone can take a short rest], up on the cargo deck Petty Office Ryeback and his team of students have prepared a cold luncheon for you all and are getting ready to start on dinner. Veena and Eris are passing through the large middle space of the command deck, platters of sandwiches in hand, when they notice faint sounds, like the distant clang of metal on stone, coming from the circular hatch in the middle of the floor. 

"Great job everyone! Here's to a space crew's hard work!" Eris pipes up as she hands the crew sandwiches to the others. When making her third return and hearing clanging of metal on stone, her cat ears twitched as she senses something disturbing. "Guys..." Eris nervously says as she runs back to the command deck and jots down some more private notes. "Me and the elf girl behind me have heard something disturbing. It's like..." She makes a series of hand and tail signs as her cat ears twitched again. "Something metallic scraping onto a rocky surface. The resonating sound of metal cutting stone..." She then goes back to sentry mode after finsihing her snack. "Everyone... keep a look out for the intruders that are with us, or any extra traps in here, got it?"

Where does this hatch go? would it be the room below or to the outside?

I think you can see on the map that the hatch is marked with a dotted line on the command deck map, and it leads to the so-called "hollow deck", the semi-open-to-space inner surface of the "bell" of the asteroid the ship is carved into.

[The Trekkie in me is angry that they didn't use "hollow deck" for the simulation chambers, as a "holodeck" pun.]

(Is Princess able to hear the commotion ?) 

Icarus moves back and yells to Princess "Can you see who is on the outside of this door making the commotion?"

He moves back to being in range of the hatch and readies his crossbow. 

Having had her attention called to it, Princess can easily focus her ship-wide point of view on the hollow deck. This deck is one large, bowl-shaped chamber containing several large piles of mechanical parts, with many more parts strewn across the floor. Several partially disassembled autognomes are among the wreckage, and picking them apart are three insectile creatures made of gleaming metal.

The creatures periodically make clicking noises to each other that sound oddly familiar to Princess, and occasionally seem to find particular part they're looking for, and carry them over to the inert form of a fourth, partially-assembled companion.

“Oi frankenbots in de old! Zoide ey makin nother ou ye kin.”

Princess tries to think where she may have heard that noise before and might have seen these things before.

(Oi frankenbots in the hold! Zoide they are making another out of your kin.)

Icarus will charge up and out the door and fire at the creature dismantling the autognome. 

Attack: 26 Damage: 9

*Ha! A fight!*

Da'Kal grabs a sandwich in her false hand and draws her battle axe.

Initiative 23

"So that's what was making the noise!" Eris exclaims as she touches her cat collar and readies her pistol and her giant hammer. "Ica-chan! Be careful! Everyone else, hold your ground!"

Initiative: 18