spoilers, read at your own risk!
SS2 is based on the UNN Von Braun, the Rickenbacker and the worm that surrounds both ships.
you play as a man who has accepted to use cybernetic implants wired directly to his skull, and metal armour. after you come out of cryogenics tube, you instantly throw up then recive a message from a person named Dr. Polito, you have been given a task to reach deck4 (Operations), when finished talking, a radar dish hits the glass destroys it and force fields activates, you immediatly head to a safe zone the door locks and the area behind that door is now in 'Hard vaccum', you continue on your way, you find nanites to buy stuff from replicators and cyber modules to buy upgrades for your implants, shortly after you find a card for science and medical, you encounter a Hybrid, the first of many monsters from the unknown, witch appears to be crew members that went insane, you find an elevator to find out the main power is offline and the only way to get to the power is via ladders and corridors. after killing cameras and monsters, you then find a bulkhead, either one with a dead power cell or one with a camera hidden around the side up agaist the wall. right now you will take the dead power cell route, after deafeating some turrets controlled by a computer thats gone insane!, Xerxes for what reason this machine has gone insane is not yet known, you find an objective get the Deck 2 crew card and shove it in the card point, after that you go find and kill monsters you find a log then you goto find Dr. Grassi, he tells you certain stuff you pick up two logs off his corpse, you then head to engineering after destroying a maintance droid.
in engineering you find out that the ship is leaking coolant everywhere in the main corridors leading to and from the engine room to security and elevator, you head through these corridors kill some monsters then continue on past a node (xerxes core), straight through corridors all the way to the bulkhead, after the ride in the bulkhead you encounter a race of spiders and flesh monsters, what they is 'will you join us will you remove these metal implants and armour?' then then proceed to the engineering bridge, then then find out you need a electronics card heading all the way back to Aux. storage room you then find the card and head back to the engineering core fit the card in, you head to fludics control only to find you need an access code witch is found in the cargobays, after picking up the code you restart fludics control witch purges the coolant from the main corridors, you head all the way to the engine core and power control only to find out you need to reset both port and starboard engines once that has been done you restart the core and power is on, you head back to security and elevators, then you head to deck3 (hydroponics).
when you reached deck 3, you cant advance to ops level because there is ant-matter blocking the elevator shaft!, you have been given a task to find, research and plug toxin-a into envionmental control systems, once you finished there kill all the enemies including eggs that look strangly simiar to alien's version of egg, then avtance to ops.
deck 4 or ops is where all the main activity goes on, you find a dead body witch is DR. Polito!, you been setup, the walls come down and a computer known as shodan announces itself, then tells a shorty of where it came from, after that you get a email, you then find and plug the simulation cards that were found on assasssin, into each of the four machines (different coloured slots for each of the cards), after you done that you pick up the main security station card and reset the security protocols... to shodan... after you finished in deck4 then find the elevator and head to deck 5.
once in deck 5 you go upto a window and see a man that is still alive! he talks to you then runs off, then head through a door, you have been given your marching orders to setup a message on a transmitting beacon that is in the athletics sector the only problem is you need to find the card, once you found the card you then need the activation code, you go around deck 5 to find the activation code on each art panel, after a long trek around the ships deck you then activate the beacon. now you have given more orders to reach deck 6, do whats nessisary to reach that level.
on deck 6, witch is command and shuttle control (includes escape pods), you must find a way to get to the Rickenbacker umbilical, your orders are get to command and set everything right, on this level your not the only human that has survived, there are 2 people that are in love and want to make it off the ship!, you must get the access card for the bridge control, witch is found on Cortez the one who is escaping the ship with his lover, they drop the card off after finding out that you are around on the ship!, you get the card to bridge control and kill a illusion Korenchikin who has mutated into a brain with a spine that makes these illusions that can kill you. you then destroy that tratoir captain, activate power to shuttle bay doors, destroy the shuttle that will be transporting there race in an egg to another place. then get to the umbilical.
you now on the Rickenbacker, your orders are to destroy black eggs, you go around shoot out all the black eggs, you make your way through the ship until you get a message from the captian of the rickenbacker, William Bedford Deigo, he was almost tempted by the unknowns but cut the beast out of his system, you encounter his dead body with a log tell you what is going on, you find out that shodan is controlling the unknowns!, you find an escape pod after heading to the last floor, you launch your ship into this flesh beast... the worm of the many...
you head through the worm, through its guts all the way to its brain and kill it, along the way you have to destroy nerve clusters and if you want monsters, you travel down a tube where the brain was all the way to the Rickenbacker bridge.
witch cooincidentally is now covered in biomatter and is the last level before you launched into the worm of the many, you head through shodans illusions with the help of Marie Delaroix, cheif engineer of the UNN Von Braun, you then kill shodan, after that you escape from that mess until you find shodan is on that shuttle with you!