Metroid Prime 3: Corruption Part 43: The Ninth Part of Pirate's Homeworld
Dane will want to meet you at a specific location at Skyway Access. To get there, simply exit the room from the doorway you entered in, and go straight. You will need to use that ball-flip area, and take the elevator to the top. Then take a left turn and keep following the hall.
When you meet with Dane, he informs you that a demolition team will follow you when so you can take out the seed. Apparently, four have to be left alive in order for you to start. What happens then is you need to follow his men, and defend them.
Your first step is to talk to the soldier standing in front of the new door they have made. Go in.
Transit Station 1104
You will see a terminal. Add some energy to it using grapple-voltage, and a door will open above you. Take it and keep going. You will see a commando, so take him out and keep going.
Transit Station 0203
You will then reach what appears to be a train station of some kind, and a tram often goes through it. Take out any and all bad guys here. The tram will go by, so cross over to the other side. There will be some flying bad guys, so use your missiles. When the flyers are out, cross over to another side and take out some more bad guys. There is a ramp that you should go up, and follow the soldiers to get you to a door at the end of that.
Transit Tunnel P6B
That will make a ramp come down, and you must go up the ramp, and then jump to the other side. You will then enter a red hallway, where you must take out any and all bad guys. Take the doorway out.
Transit Station 0204
Keep going, taking out bad guys along the way. Use Phazon when in a pinch. When one of your guys dies, you will hear a high pitched squeal. Help them defeat the enemies by taking out the tougher ones. For example, the ones with the shields need to have their defenses grapple grabbed out of them.
Transit Tunnel P69
Not much in this one but two more commandos. They are pretty easy to take out. One throws Phazon grenades, so be sure to fire constantly if going into Phazon Overload.
Transit Station 0205
You will also come to a point where you will see a Berserker Lord. Just remember to shoot its firing Phazon energy back at him, and he will be vulnerable. Take his head out.
Eventually you will come to a point where the last three foes will be invisible. Turn on your X-ray visor, and you will see them, and can defeat them.
The four demolition guys will then blow up the locks on the giant door in front of you. You will need to turn on the hand scanner to activate it, and it will open.
Transit Tunnel P70
By the way, there is a Phazon pool here that you can dip in and be completely replenished. You might want to take advantage of that. There will be another door you will need to open after that.
Transit Station Leviathan
In this room, there is a big machine in the center of the room that you need to jump to the top of, then jump to the green ledge. You will then be attacked by a Pirate Commando and his two henchmen. The henchmen can turn invisible, so go into X-ray mode to find them to kill them, they will go down after a few direct hits. As for the lead guy, he takes a lot of hits to take him down. Use Phazon on him when you can, and then just pack him with what you got. Eventually, his armor will break and he’ll fall apart.
Take the green ledge again. You will find a control panel there, and activating it causes the whole room to turn into a landing place. Go down a nearby hole and out to the wide area and summon your ship. You will see a prompt saying “Attack”. Your ship will come to you, and it will also blast open a door.