To Shut Down A Defense Network

Land at the Pirate Homeworld's Command Center landing pad. Take the elevator up to the middle floor here; you should've disabled the lock here that'll let you move on. (If not you'll have to go through the Command Courtyard and Flux Control to get back here.)

Shutting down the defense system will let the GFS forces raid the planet.

To shut down the defense system, climb all the way to the top of the room here and use the switch up there with your x-ray visor. That'll unlock three phazite panels on the system itself. Drop down to each one and look through it with the x-ray visor and blast the little balls there with your nova beam. After all of those balls are destroyed, return to the top of the room and activate the bombslot to let the Galactic Federation forces land.

Dane is going to show up now at a location on the planet. Before you meet up with him, though, this would be a good time to go and explore the GFS Valhalla. Completing the Valhalla isn't entirely needed to complete the game, but it may influence your final ending. You can also pick up some extra pickups on the Valhalla, so if you're looking for the 100% pickup ending, you'll definitely need to explore it thoroughly.

Meet With Dane

If you do want to go ahead and meet with Dane now, you can do so. He's in the Skyway Access point in the Command portion of the Pirate Homeworld. Speak to him, and he'll give you your task: reach the access node for the Leviathan Seed here on the Homeworld while escorting Demolition Troopers that will be needed to blast the final door away from its hinges.

Use your hypermode to overwhelm the enemies during this section.

Wait until the first demo trooper opens the door to the Transit Station, then follow through and use the grapple energy to charge up the doorways leading on. Transit Station 0203 will be the first place you have to protect them in, as multiple pirates will appear and focus on firing on the troopers instead of you. It's relatively easy to protect them all if you use hypermode to quickly blast away at the pirates as they appear; there'll be a few containers where you can restore your health if need be.

You'll need to repeat this process in a couple more rooms before you reach the end. Again, just use hypermode to blast your foes and ensure the troopers survive. You don't need to keep them all alive; only four out of the twelve actually have to live. In the third room, you'll face off against a Berserker Knight. Kill the regular Pirates here first, as they'll be targeting your friends, then start reflecting the bomb shots back to the Knight's head and finish him off after it pops off.

Who's Running This Show?

When you get past the large door, you'll reach Transit Tunnel P70. Drop down into the phazon here and absorb it to rehealthify yourself; you'll want a full health bar before using the access terminal above the phazon that'll lead you into Transit Station Leviathan.

Why? Because, when you jump up to the upper level of the transit station and attempt to use the grab ledge, you'll be accosted by the Pirate Commander. This guy isn't anything severely threatening--he doesn't even get a boss fight life meter--but he can be quite an annoyance, thanks to the fact that he has several commandos accompanying him. The commandos will phase in and out of view and generally be a huge annoyance to you, but you will probably want to deal with the Commander first, since he'll often hit you with hypermode shots that will quickly drain your energy.

Hypermode: what can't it do?

Counter this strategy by flipping into hypermode yourself. If you can get a bead on the guy, then hyper missiles or regular hypermode fire will eventually destroy his armor and let you finish him off. With that done, switch on your x-ray visor to follow the commandos as they shift around and repeat the process with your Nova Beam.

When the Commander has been decommissioned, flip back up to the grab ledge and use the machine there. That'll let you use the command visor to call down your ship and have it attack the barrier leading on. With that done, you can enter the ship and select the Seed as your next destination. But first, now would be an opportune time to explore and conquer the GFS Valhalla, assuming you've managed to find all of the energy cells.