You've finally reached the last stage in the game, and it's time to put the mad doctor in his place and rescue your creator. First, though, you have to get to the battle. Though this stage is quite short, the few enemies that occupy it are pretty good at draining your life ahead of the big battle.
From the start, head to the right and you'll find one of the roaming mech tanks. Jump and shoot it in the crystal eye with a charged shot or two while avoiding its lasers, then press onward.
Next, you'll drop through an opening to a ledge below. Face left and let loose a charged shot at a waiting turret before dropping from the edge of that ledge and falling to the area below you. There, head to the right and you'll find a second mech waiting. Defeat it the same way you did its predecessor, then head through the gate it was guarding to face the final battle.
This fight takes place in two phases, but neither of them will last particularly long if you're doing things right. One thing to keep in mind is that you have no way to refill your E-Tanks if you happen to use some of them and then die, so practice up for a bit until you're good at the fight before you start dipping into your reserves.
In the first phase, you'll find yourself at the greatest risk. The Skull Tank takes up most of the right side of the screen and pelts the left side with heavy firepower that does a lot of damage when it connects. There are blue bouncing balls that you can slide under, and red napalm that you can jump to avoid. Between shots, the tank also likes to try and suck you toward it using a powerful vacuum.
The easiest way to counter all attacks is to launch an offensive of your own using the S Arrow weapon. Jump and fire it at the tank's mouth when you can do so without taking a hit, then focus on remaining at a distance while your shot does its thing. It should find its target and inflict a lot of pain on the tank, even if you're busy sliding away from the scene to avoid the suction attacks. Then you can repeat the process as needed.
When you deal enough damage, Dr. Wily will separate from the main tank and his craft will turn invisible. This is the point of the battle when it makes the most sense to use one of your E-Tanks if you need to, typically.
Switch to Beat and let him fly around and take care of Dr. Wily while you dodge attacks. Wily likes to fire a shot straight down that hits the ground and splits, so try to avoid positioning yourself beneath him when he appears, and be ready to jump the shot as it zips toward you along the floor. Also try to keep your distance from the tank, because next a series of aura balls will circle around it in a spiral pattern. The good news is that you can tell where Wily is shortly before he attacks because Beat will head toward that section of the screen, which makes it easy to stay out of range.
As long as you manage to stay alive for a bit, Beat should take care of the rest and the battle is easily won. If you die at any point, though, you'll have to return to the start of the stage and start fresh.