You are hired by Elisha Kettel to recover the IRIA Ruby from the ruins of Nara. To kick things off, go to Gyori and enter the Kettel Industries headquarters by the stairs. Talk to Elisha Kettel; likely as not she'll give you the mission to recover the Ruby from the ruins of Nara. If you have joined up with another corporation, then the way down will be blocked by steel bars. Don't worry, though; if this has happened (or if Kettel hasn't given you the mission), you can still recover the Ruby and sell it on your own initiative. (You may even make more money by doing this than you would if you sold it to Kettel.)
Peter: I find the ruby more interesting for giving you a bonus point of Knowledge and the 150 SkillXP in a few skills. My characters tend to be good guys who decide to protect the ruby from Elisha Kettel, by agreeing with the head cyclops to keep it a secret. This doesn't stop you from accessing data from it, though. Just use it without picking it up.
If you are employed by Kettel Industries, getting the Ruby for Kettel will basically get you promoted by 1 rank. (It gives you 500 facXP, but facXP resets to zero after every promotion).
In order to retrieve the Ruby, you will need powerful weapons and armor, good combat skills (especially Dodge), a high Perception stat (cyberware is useful here) and good Investigation skills. Also useful are the Code Breaking and Athletics skills. You will find it quite difficult without one or the other. Stealth and smoke grenades might work as well as running for escaping the cave if you want to steal the ruby.
Another thing that will help you is if you retrieve the Primal Genome for Forager in the ruins of Markheim Fortress. This will cause the cyclops guardians to trust you. If you don't do this, then you'll need to do a lot of fighting.
When you have the necessary items and skills, go to the ruins of Nara. (They are to the north-east of Gyori, and can be easily reached by mecha. Have a peek between a range of mountains and the sea, and you will find it.) Once inside, you will have to contend with several dangerous types of biomonster, including Morlocks and Hunter-Synths. Fight off the monsters--or run away--and search for a locked building. When you've found it, batter the doors down or use your Code Breaking skill on them and enter.
This is where your Perception stat and Investigation skill will come in handy--as, if they aren't high enough, you don't have a hope in hell of finding the trapdoor that goes down. Search the building. When you find the trapdoor, enter.
You will be hailed by two cyclopses -- the guardians of the Ruby. Tell them you are there to talk to their leader. They will allow you to continue on if you are very heroic, have completed Forager's task, are very lawful, or you make a Conversation skill roll (beating a target of 12). If you are refused entry, you can leave, come back, and try again without starting a fight.
The stairs down to the cyclops city should be quite close to the stairs you've just used.
In the cyclops city you will find lots of cyclops guards and the cyclops leader, Praetor. If you talk to him, you probably shouldn't admit to him that you're going to steal the Ruby. If you just want to access data from it, you can talk to him and agree to keep it safe, so you can lie to Kettel without becoming Chaotic. You can also talk him into giving you the Ruby and letting you walk out. You can do this if you're a member of Hwang-Sa and you're willing to burn your bridges (FacXP -500. Ouch.), or with good Conversation (skill level required: 9).
Other than the citizens, there is a computer terminal, and the Ruby itself. Picking up the Ruby will set off an alarm and the cyclopses will attack you. Using Code Breaking on the computer will disable the alarm. However, the guards on the level above WILL still attack, so be prepared to fight or run.
If you set off the alarm, RUN as quickly as possible to the exit. You probably want to have a route planned out, and maybe even some smoke cover already laid down. A smoke clip in a havoc legging works well, as do heavy smoke grenades. The cyclopses are armed with Pin Cannons and Bioswords, both of which cause serious hurt, so running out of Stamina can be positively deadly. This is where Athletics comes in extremely handy.
If you're going to fight anyway, kill a cyclops and take their weaponry. It can be extremely useful if you have the right combat skills. BTW, the Cyclops Progenitor is SF:1, so you can't pick up his weapons!
When you have exited the city, run the short distance to the stairs leading to Nara, then exit Nara. Congratulations! You have now absconded with the IRIA Ruby and possibly placed all of humanity in grave danger. Good for you. Take it to Elisha Kettel or sell it to get your well-deserved reward. Or just keep it in your mecha inventory to make your mecha more valuable, so you fight tougher opponents when the game scales your opponents by your own PV (which is most of the time).
You can also try and get the data out of the Ruby by using Science on it. To succeed, you need to make Science, Code Breaking, and Concentration skill rolls. Skill rolls on items (or in plot scripts in general) always use TeamSkill, so skilled lancemates can do it for you. Bring in the professor!