After you land on ZDR, you are knocked out by a mysterious enemy, and awaken to find your Power suit diminished.
Reach a Network Station
Go to the right (the door to the left can't be opened right now) and kill the creatures along the way.
Hold ZL while running to slide through the gap in the way.
Hold L to aim and kill the red thing in the ceiling above the door (which can't be opened right now). Climb up to where it was, and make your way along the straightforward path, but watch out for the creatures that shoot out of the ceiling as you make your way along the path.
Hold L to aim and shoot the glowing blocks in the wall, then jump and grab the gaps where the blocks were.
Stand on the glowing panel in front of the statue to the left to refill your ammo. Red statues like this are Ammo Recharge Stations.
Jump up to the right, shoot the missile block with a missile, then go to the right and shoot the lowest block of the wall with the normal beam. Go right and avoid the creatures that shoot out of the ceiling. Shoot the door to open it, and go through.
You will get a briefing, and afterward you will be asked if you want to save. You can always save in rooms that are marked yellow on the map.
Get a Missile Tank
Go through the door on the right. Go to the bottom and kill the slug creature in the way. At the bottom, go to the right and slide through the gap on the right.
There will be a brief cutscene that teaches you how to parry, aka melee counter. Watch enemies for the flash, which is accompanied by a sound effect. If you are close to the enemy, you can press X when that happens, to perform a Melee Counter. Always shoot your beam or missiles (without holding the aim button) after a successful Melee Counter. The Melee Counter is important, so don't forget.
If you haven't already, press X to proceed, then shoot the normal beam until the enemy is killed. The enemy will drop more items if you use parry, so use it at every opportunity.
You can also press X while running to do a Dash Melee attack. It does a small amount of damage, and can kill weaker enemies.
Go to the right side of the room and make your way up the platforms. When you reach the top of the area, there will be a cutscene explaining how to find hidden items. The map will blink to indicate areas where there are hidden items. Exit from the map, then shoot the red thing in the wall and you will reveal an area with a missile tank. Collect it to increase your missile capacity by 2.
E.M.M.I.-01P (Broken White E.M.M.I.)
Shoot the door on the right and go through. You will fall down a chute, and there will be a cutscene. It tells you that although you can counter an E.M.M.I.'s attack by pressing X at the exact moment of the flash, the timing is extremely difficult, so this is unlikely to succeed. This time, however, it is guaranteed to work, so press X now.
Afterward, you are instructed to tilt the left control stick and press ZL to slide under the E.M.M.I., so do that. Avoid physical contact with the E.M.M.I. at all costs. If you make physical contact with an E.M.M.I., you will have to perform a Melee Counter at the exact moment of the flash as described above, and if you do not succeed, you will get a Game Over. However, if you do get a Game Over, and choose Continue, you will start at the last checkpoint, which is usually not very far from the encounter where you were defeated.
As soon as you have slid under the E.M.M.I., shoot the door on the right and go through it. Keep going to the right, and at the end, jump up the ledges. There will be a brief cutscene where the E.M.M.I. follows you. As soon as that cutscene ends, go to the right to go through the door.
There will be another cutscene, where your Arm Cannon is transformed into an Omega Cannon. You are instructed to hold L to switch to Aim Mode, and tilt the left control stick to aim, so do that now. Then you will be instructed to hold R to charge up the Omega Cannon, and aim it at the core (i.e. the glowing red thing on the door). When it is fully charged, press Y to fire at the glowing red thing on the door.
After the door opens, go through. Go to the left, and the E.M.M.I. will come through the door. Go toward the right, but don't jump back up to the ledge. Instead, hold L and R to charge up the cannon, and when your cannon is fully charged, aim at the E.M.M.I.'s head and press Y to shoot. If you can't charge it up in time, jump up onto the ledge and slide through the gap on the left so you can go to the left and put some distance between you and the E.M.M.I. so you can try again.
Continue to the Next Area
After the E.M.M.I. dies, the Omega Cannon will revert to the normal Arm Cannon. Go through the doors on the left until you are back in the cave. Go up until you reach a door on the left. Go through and stand on the glowing panel until you are asked to save your game. Press A to save. Then go through the door on the left.
Kill or avoid the creature on the wall on the left, then go downward. You can't open the door on the right, so go left. Press ZL to slide through the gap on the left, then jump into the water and aim to the right, at the red thing in the stone on the right side of the pool. Then jump up and grab the the ledge on the left. When you pull yourself up, there will be a cutscene where you go through the door that has small floating cubes in it. This door leads to the E.M.M.I. Zone patrolled by E.M.M.I.-02SM.