With the true mastermind revealed, now you can finally make some real headway. This is the last of the truly difficult stages you'll face, and yet it's also a great place to prepare yourself for the final leg of your journey.
In the starting room, you should notice an E-Tank within easy reach. Check your inventory and see how many of them are already in your inventory. It's not a bad idea to have five or so on hand for the rest of the journey, and 9 is even better. The good news is that you can hop up and grab this one, then head down a single screen and kill yourself on the spikes that line that vertical passage. Lose all your lives, continue, and you'll find that the E-Tank has returned. You can abuse this setup to quickly build up your supply.
When you're ready to proceed, you'll have to drop down that shaft while avoiding spikes, but it's not terribly rough. Keep to the middle as you fall to the next screen, where you'll land on a ledge. Drop off its left side and hold slightly right as you fall into the next screen, and then continue to hold toward the right as you drop, so that you land on solid ground at the base of the shaft, rather than the bed of spikes.
Continue to the right now and you'll have to jump to avoid some enemies that roll along the passage. Beyond them, you can ascend along some ledges while taking out red lobsters with charged shots from your arm cannon. Then climb a ladder into the next screen.
This room is crowded with enemies, but they'll all fall easily enough to more charged shots. There are turrets that pop up along the stairs, as well as armored bats. You've dealt with these guys numerous times throughout your journey, so they shouldn't pose a threat now. Defeat them and then climb another ladder.
When you begin to the right in the next area, you'll see spikes along a low ceiling. You can drop down and defeat another lobster enemy, then hop past where he was positioned and run right along rotating wheels. Don't jump, as the spikes are no less lethal here than they are everywhere else in the game. Keep your head down as you advance slowly through this area, taking out foes with charge shots. Then climb a ladder.
In the next room, a bunch of floating pods will rush you. It's easy to take them out a few at a time with charged shots. Then you can use Rush Coil to reach the ladder and climb into the next room, which also triggers a welcome checkpoint.
This is a tricky area, because there are more of the spinning wheels, only now they're not in groups. The idea is that you need to jump from one to the next, using them to carefully make your way toward the right while avoiding enemies that occasionally circle them, and another foe that looks like a floor buffer and fires spread shots in your direction. Keep going, and you'll either make a long (and difficult leap) to a set of wheels on high ground, or you'll have to make strained leaps along a lower route. This process can require some practice, and if you have too much trouble, you might just want to use the Rush Jet to cheese your way across the abyss.
When you reach the far side of the pit, you'll soon pass into a new gauntlet reminiscent of Dust Man's stage in Mega Man 4. Huge, crushing columns descend from the ceiling, then ascend and repeat. You have to advance along the passage, shooting enemies and occasionally debris that blocks your way forward. If you let a column come down on you, it's every bit as fatal as falling into a pit, but you shouldn't have much trouble if you pay attention and take things slowly. A couple of quick slides back to back will allow you to advance quickly, as well, in a pinch (start sliding just as the next set of columns begins to rise). Just make sure that you've cleared any debris out of the way first. The last set of crushing pillars can only be passed with a series of three slides in rapid succession.
Once you make it to the end of that dangerous gauntlet, you'll appear in a small room with a rooster enemy positioned along some high steps. Shoot his eggs to refill energy if you wish and then get closer and jump and fire at his beak to eliminate the mechanical bird himself. Then ascend another ladder.
The next room is a simple one with more pods you can destroy, and some turrets along stairs. Eliminate them with charged or standard shots and climb a ladder into the next room.
Now you're at the left side of a horizontal shaft. Floating enemies are approaching from the right, and guarded turrets are positioned along ledges that rest between small, shallow pits lined with spikes. You can advance cautiously here, taking out the turrets when they raise their shields. When you reach the far side of the area, you'll find the gate that leads finally to the boss.
This boss looks fearsome and at first seems invulnerable, but he's actually not all that tough.
You'll notice as you enter the area that your boss is shaped about like a column, with a head on top. The head is his weak point, and the column is in segments. Shoot the lowest section of the column and it will fly toward you. Hop quickly and you can land on it, then shoot the next segment and repeat the process. Then quickly charge a shot and jump and shoot at the head to deal some damage with your arm cannon.
You'll need to repeat this process until you win, but matters are complicated by the regular shots your foe fires into the air. Small green pods disappear briefly from sight, then rain down on you from above. They don't fall in a straight line, but rather swerve back and forth, so you have to be careful of them while you're trying to gain enough altitude to get in some good shots.
Though the fight can drag on a bit, there's not really anything more to it, and patience will lead to victory.
NEXT: Stage Two