Go to the room under the house where you incubated the egg, and notice a generator covered by a green tarp to the right of the incubation machine. Wait for a Valkyrie Drone to spawn, and kill it near the generator so that it explodes nearby. The generator will now turn on for a limited time. If you fail to acquire the cylinder in time, go back to the generator and interact with it to restart.
[generator]
Around the map are six valves; one of them has a green light above, and one of them has a pink cylinder floating around inside the valve. Note these locations, and input them into this website. It will give you a list of numbers to change the valves to around the map. If you've done this correctly, you can return to where you saw the cylinder, and it will be available for you to pick up. Here is a map showing the locations of these valves on the map:
http://www.kronorium.com/img/locations.png
Go to Dragon Command and go up to Sophia. Interact with her and wait for her to finish speaking. You can then place the cylinder into the machine. Letters should now show up vertically on the machine, and you must type in a password by shooting the letters to change them. The password is KRONOS. With the password ready, interact with Sophia again.