The SC will inform you of X activity in Sector 2 (TRO), so we'll be heading over and investigating that area now. Go back up to the Main Deck and head over to the Sector 2 elevator. Ride it down and go into the Navigation Room. Here the SC will give you more bad news, it has figured out what's been hacking into areas on the station. The creature you saw earlier is the SA-X, an X parasite mimicking Samus.
Never before has Samus been in battle against her own abilities, so you'll need to be very careful around the SA-X, it's a deadly adversary. The computer will tell you to run if you encounter the SA-X, as it'll be able to freeze Samus with the Ice Beam.
You'll now need to download the Bomb data, but the Data Room is blocked by a Level 1 security door. So first we'll need to track down the Security Room to unlock Level 1 doors. Sector 2 looks fairly small when you download the map, but most of this area is hidden and you'll have to map it out yourself.
Go right and use the Recharge Room if needed, then go right again. You're now in a large green room filled with red crawling critters. Blast any you encounter and climb up to the top right corner of the room. Head through the door there and cross the next vine-filled corridor to reach a shaft leading up full of vegetation. Ascend the shaft and go through the topmost door to reach the Security Room.
Drop down to the station below and stand on the pad to unlock Level 1 Security Doors. Now you'll be able to access blue doors, so use the one on the right to exit the room. Head back to the large green room filled with red creatures and go through the blue door down on the bottom left corner. Cross the next corridor to reach another large room adjacent to the Data Room we need to get to. Climb up to the top left corner of the room (watch out for flying bugs) and head through the door to reach the Data Room. Step into the pod to download the much-needed Morph Ball Bomb data.
Now you'll be able to lay bombs while in Morph Ball mode. Leave the room and go back down to the door you entered the previous large room via. Just as you enter the room though you'll hear an explosion and footsteps fading away - the SA-X has just been here and thankfully missed you. The downside is that it destroyed the door you used earlier, so we'll need to detour around hidden areas in this sector to get back to the entrance.
Before you go anywhere, bomb open the small cracked wall up in the top-right corner of this room to find a hidden tunnel leading to Missile S2.01. Now go down to the dead-end in the bottom left corner and lay a bomb in the corner to open up a passage leading down. Drop down to find yourself in a corridor with two doors leading off. Save your game in the room to the right before going through the left door. The next room contains a large shaft leading down, you should notice on the map that you've entered an uncharted (green) area, this is only the tip of the iceberg. Before descending the shaft you'll be able to find Missile S2.02 up the top. With the missile in hand descend the tall shaft and head through the door at the very bottom.
Drop down the next short shaft and head through the next door to reach a large room full of more vegetation. bomb the platform in the center ahead to fall down below, but watch out for the Sidehopper there. As you go through this room you'll be able to pick up Missile S2.03. With the missile tucked away head through the door on the right side of the room. Cross through the next corridor and bomb around the ground in front of the tall pillars to cause smaller pillars to rise up, use them to get through. The next room contains yet another tall shaft leading up with several doors to choose from.
The door directly ahead eventually leads to a Save Room, don't bother going in there if you're playing for speed. Climb up the shaft and head through the door just below the open door on the right wall. Cross the next corridor to find yourself in a smaller shaft. There's a hidden door down below in this room (shoot out the ground to find it), but we'll be going straight ahead instead. Save your game in the next room before proceeding. Cross the following room to find yourself in a room with two red critters and Energy Tank S2.01 sitting atop a platform in clear sight.
Grab it and shoot out the floor at the base of the platform. Drop down to come face-to-face with an Eyeball Door. Fry and go through the door. In this next huge room you'll face another Core X boss (a tall creature with one big eyeball), refer to the bosses guide for tips on taking this weird thing down.
Once the creature's dead you'll recover both the Hi-Jump and Jumpball abilities together, so you'll be able to jump higher as well as jumping while in Morph Ball mode. Exit the room the same way you came in, it's time to return to the Navigation Room. When you jump up into the small room where you found the Energy Tank you'll notice that the red critters look like frozen statues on the ceiling and wall, it seems that the X are trying to change their forms by cocooning themselves. Save your game on the way back, eventually you'll reach the long corridor connected to the tall shaft you climbed up earlier.
Blast the Sidehopper here, but you'll find the door's been destroyed by something, so you'll need to find a way around. Bomb open the rubble at the foot of the door and drop through the floor. You'll drop down into a darkened corridor, stay exactly where you are as just below the narrow platform you're on the SA-X is prowling around. This is your first true encounter of this freakish creature, make sure it doesn't see you. The creepy music and the ghostly footsteps the SA-X makes will make you shiver, just wait it out and it'll leave via the door on the left.
Once the SA-X leaves, go over to the right and shoot out the floor to drop down into the room. Proceed out to the large shaft and climb up. Here you'll spot more of the red critters hibernating, they won't emerge yet though. Directly opposite the ruined door you'll find a room that leads to Missiles S2.04 & S2.05 (you'll still be able to reach S2.05 without the Gravity Suit). With both missiles in hand ascend the tall shaft, using the hibernating creatures on the walls as stepping stones to reach the higher platforms. Head through the door at the very top and through the next room to find yourself in another shorter shaft. Blast the Sidehopper there and climb up.
You can find Missile S2.06 hidden beyond the small tunnel on the right wall here. With the missile tucked away go back to the shaft and roll through the small opening on the left to make it back to the large green room near the entrance. Before heading back to the Navigation Room you'll be able to find Missiles S2.07 & S2.08 from here. Once you're ready head back to the Navigation Room for your next objective.