This is a substantially difficult stage, far more challenging than any before it. If you died in the previous stage, you'll need to do your best to attain a good level of firepower, or this stage will be next to impossible. Similarly, if you die at some point in this stage, your chances of reaching the end are very small.
- After a pre-stage which only offers six opportunities for power-up capsules, you will approach the ship which deposited the bosses throughout the previous stage. Now you will need to shoot at the hatch in order to blast it open and proceed inside. As was the case for the final stage of the original Gradius, you will be flying through a large space fortress. This fortress will contain many enemies along both the top and the bottom of the stage, often through narrow corridors. All of the four power meter arrangement but the second have the ability to shoot upward, whether it's the Double weapon of types 1 and 3, or the 2-Way Missiles of type 4. Making use of these weapons will improve your chances of survival. Only type 2 lacks an upward fire. While its incredible firepower may have enabled you to reach this stage, this one weakness will become evident here.
- As you fly through the stage, it's a good idea to remove the prepositioned enemies as quickly as possible, even if that means flying closer to the right side of the screen. The threat that remains after that is the Duckers who walk on to the screen from the left and follow the terrain of the ship up and down. Shortly after the stage begins, there is a hatch along the top in a blind corner that is difficult to shoot. This is followed by a narrow tunnel completely filled with cannons.
- After you make it through this tunnel, the stage will open up and Zabus will begin to materialize. At first, only single columns of them will appear along the right side of the screen. Then a group of them will appear across the entire screen at once. After they begin to move toward you, a flood of them will appear from the left side of the screen. Be on guard when they appear, and move out of their way if you can't destroy them with your Options.
- Once the Zabus stop, the next challenge will begin: the tiles along the floor and the ceiling will rip off from the surface and fly straight towards the Vic Viper as if drawn magnetically to it. Dodging along won't be sufficient, you'll need enough firepower to cut a path through the tiles to survive this attack. You can preemptively destroy the tiles before they leave the floor or ceiling with your weapons. Note that while this occurs, two enemies will bounce in from the left. When they travel far enough to the right, they will simultaneously fire bullets in a circle all around them.
- After you survive the flying tiles, there is a short distance through a bit more of the fortress where flying enemies, combined with hatches and cannons along the terrains, attempt to prevent you from reaching the middle of the stage, where you will encounter the first considerable challenge; the Intermediate Fortress. You will know you have arrive when the floor and ceiling disappear, and a large orb crosses the screen from left to right.
- Once the entire array is assembled, there will be a series of small guns surrounding an opening to the core, which is ultimately filled with barriers. Two domes along the top of the bottom open intermittently to release Duckers. The guns fire small bullets that can fill the screen and make it particularly difficult to find safety. If you make it here with at least two Options, you can attempt to adopt a strategy to stay safe, remove the guns, and attack the core, but it truly takes all four Options to remain motionless throughout this fight. Fly from the top to the bottom, or the bottom to the top, and spread your Options out so that the second one is firing down into the barriers, and ultimately the core. The first and third options will end up destroying the gun array, while the Vic Viper and the fourth Option shoot any Duckers that attempt to escape from the dome. With some patience, you will wear down the barriers and destroy the core.
- After the battle with the Intermediate Fortress, you will begin another gauntlet to the next challenge. You will return to regular fortress combat conditions, except that now different parts of the floor and ceiling will rise or lower to particular heights, creating new channels for you to fly through. Once again, having the ability to fire upward is extremely helpful here, and Duckers approaching from the left are particularly dangerous. When narrow tunnels appear, try to remain inside them for as long as possible to use them for cover.
- Once you reach an are where the floor and ceiling level out and the enemies stop appearing, fly over to the right. Duckers will begin to appear above and below, while the next major challenge approaches from the left: Crab. Crab is a large purple machine whose height extends from the floor to the ceiling. It has six legs, three on top and three on the bottom, and it makes its way from the left to the right. It is indestructible, and you'll only means of survival is to avoid colliding with its legs. This means committing the Vic Viper to the top or bottom half of the screen, and slipping beneath the legs as they lift up and advance to the right. Crab has no weapons of its own, but the Duckers which appear on the floor and ceiling will be shooting bullets at you, and these bullets can pass through Crab, so be careful.
- Once Crab reaches the right side of the screen, it will hesitate, shake its torso, reverse course and return to the left. Unfortunately, the game gives you very little warning about this, and because of the speed of the scroll, you only have one opportunity to fly through either of the two left most legs. If you miss it and are stuck on the left side, you will die when you collide with the legs. Once you successfully dodge the first step to the left, it will decide to go back to the right for a while. Then it will make one final change of course and commit to returning to the left. Once again, you must dodge the left legs on the very first step or you will be crushed by them before they lift again. Then slip past the next two legs as it leaves the screen. Of course, the entire time you must watch out for the bullets being created by all the other enemies which you can't necessarily get to quickly (or safely) to stop them from shooting.
- A note about the PC Engine version: Due to the decrease in horizontal screen resolution, the return trip for the Crab from the left side of the screen to the right side is particularly precarious. The left leg will not travel far enough to the right to provide the Vic Viper with safety on the left side of the screen until it has lifted and moved at least two times. So you'll need to spend a bit more time beneath the crab while it begins moving back to the left.
If you survive the encounter with Crab, you will notice the space fortress go from technological to distinctly biological. All of the enemies will cease to appear as you fly through this new organic section. Fly to the right to avoid two cellular structures which attempt to close off access beyond the tunnel. Then fly back to the left as the room opens up. You will soon be face to face, literally, with Gofer. Several stems connect his exposed brain to points along the wall. Once Gofer is fully in view and speaks to you, you can shoot these stems and destroy them. But the truth is, this really isn't a battle at all. You can do absolutely nothing and still win. After a short period of time, Gofer self destructs. You will be treated to the ending of the game, and be presented with the credits before the game starts over at Stage 1 at a higher degree of difficulty. Congratulations.