Before leaving the complex, take note of a large portable power generator resting in an alcove up in the north-eastern corner - you'll be coming back here later. Look for a small lift on the western side of the complex and ride it up to the exit. Move through to the Generator Hall North area, you're almost back to the shield generator's observation chamber.
Use Hypermode to deal with a lone Shield Pirate Trooper barring your path, then move through the winding pathway (lots of environmental detail here) and deal with the pair of Jolly Roger drones ambushing you at the small canyon. See the upright platform on the other side of the short canyon? Also see the roving Fuel Gel tanks moving about on the rails above? Shoot the fuel tanks as they pass over the platform to easily dismantle it.
With the platform gone a small control interface becomes visible on the wall, cross over and interface with it. Follow the on-screen instructions to rotate a nearby stone disc, granting you easy access to Missile Expansion BR.10. That's all for this region, so exit the area via the door down the end of the canyon to find yourself back in the chamber with the shield generator's observation window.
Don't let the pair of patrolling Pirate Troopers stop you. With your position clear step over to the observation window. Both turrets are now merely smoldering ruins, so let's deal with the generator. Summon your ship again to perform a successful attack run - watch as your ship blows apart the shield generator and the massive blue shield protecting the visible Leviathan fails completely (granting a bonus gold credit too).
Time to storm the Leviathan Seed. Travel back to the Field Access chamber and feel free to save your game nearby before heading for the Jousting Field. Once there, you'll find the area deserted save for the amazing wreck of a Space Pirate aircraft - scan the downed vehicle to learn that your recent dealings with the Leviathan's shield generator are to blame for the crash.
Being Space Pirates and all, they're far too tough to let a simple crash-landing ruin their day. Sure enough, a Pirate Militia and an Advanced Pirate Trooper hang about the wreck (scan the Advanced Pirate Trooper again if you missed out back in the Temple of Bhyyo). Deal with both and keep your ears open - hear that whining engine sound every so often? Look up and wait for it again, you'll see Space Pirate ATCs streak across the sky heading for parts unknown. Exit the Jousting Field and watch out for more Crawltanks in the Enlightened Walkway.
Move back to the Ancient Courtyard to spot more Pirate activity. An ATC tries to lift off and escape, quickly shoot it down using Hypermode and gather up any health and Missile refills it drops. Step inside the Overgrown Ruins region to find it curiously devoid of any patrols. Return to the Thorn Jungle Airdock and hop aboard your ship.
Hit the center console once aboard, this time the Leviathan Seed is well and truly selectable. Select the Bryyo Seed and watch as Samus lands aboard the Phazon vessel, entering a region even more alien to the Bryyo environment (if that's even possible). The innards of the Leviathan are teeming with Phazon growths and a healthy blue glow over just about everything. Just imagine, if left unchecked the entire planet could eventually look like this.
Upon landing you should probably hop back in your ship and save the game now for convenience. Step forward to the edge of the small landing pad and look down at the floor of the chamber, see the Scorchbugs roaming everywhere? As odd as it sounds, if you stay here and clear every last bug you'll receive a bonus Friend Voucher.
Scan the Phazon growths around the vast chamber to learn more about this eerie realm. Now let's move deeper into the heart of the Leviathan. See the floating platforms strategically placed in the chamber? Leap across them to reach the exit on the far side. Scan the Leviathan Door before opening it (check your Logbook - it mentions bone plates retracting as the door opens...). Open the door and step into the winding tunnel beyond.
Right ahead of you lies a mass of organic Phazon twisted together to block your path. See the huge roving eyeball? Enter Hypermode and blast the eye to clear the obstruction. Move through the twisting corridor (don't forget to take in the scenery outside the tunnel) - two more of the organic masses block your path. Use Hypermode to clear both, but you may wish to return to your ship and recharge if you use up too much health.
Once you're ready, exit the Core Access tunnel to reach the Bryyo Leviathan Core (that was quick). This gargantuan chamber houses the Leviathan's core up in the ceiling - and that massive stone monster in the center of the chamber - the one on the receiving end of a massive Phazon shower - is your only obstacle to shutting this Phazon factory down.
Before leaping down to face your challenge, look at the walls either side of the door. See the orange-tinged Phazon growths? Looks a bit like the orange environment found in the Impact Crater back on Tallon IV...
As you land at the base of the chamber, the Leviathan Seed will awaken its guardian - the monstrous stone Golem known as Mogenar. This massive artificial creature once served the last Bryyonian Lord of Science during the planet's ancient wars - now it serves Phazon. You're in for a tough fight (most especially on Hypermode difficulty - be ready for one of the toughest boss fights in the game), so refer to the bosses guide for tips to conquer this mighty alien machine.
Upon besting Mogenar - Samus is in for some good news and bad news. First the bad news: by destroying Mogenar and releasing all the Phazon energy built up inside it, Samus receives a massive dose of the the poison - elevating her internal Phazon corruption (you'll see a view inside her body as gross Phazon cells enlarge slightly). The effect it has is visible on her PED Suit - the suit now has a sharper tinge of blue around the edges.
Strangely enough, in a hostile and extremely dangerous environment no less, Samus removes her helmet, revealing her face. But before you think it's a reward for conquering Mogenar - the camera pans out as Samus literally throws up - further highlighting the extreme danger of Phazon corruption poor Samus is enduring.
But that's it for the bad news, as once you regain control you'll find a glowing blue upgrade waiting where Mogenar once stood. Scan the item to reveal it as the Hyper Ball - every time you conquer a Leviathan Seed's guardian you'll be granted a new Hypermode ability. Pick up your prize and watch as Samus glows crazily blue herself.
You'll now enter a permanent (but completely safe) state of Hypermode as a number of gross Phazon growths pop up out of the ground nearby. Time to deal with the core. Activate Morph Ball mode and hold A as you move around to each growth - the Hyper Ball's electrical attack will make short work of all your targets.
With all targets cleared out, a massive burst of Phazon energy streaks toward the core's underside before the disgustingly massive beast emerges itself. The core resembles a huge brain, covered in numerous blue eyes and sporting a number of large pincers. Strangely enough the core can't defend itself, is simply hangs in the air while Samus' body temporarily overcharges with Phazon energy. She'll float into the air herself before you return to her view. Unable to move, the message "PRESS A TO RELEASE PHAZON ENERGY TOWARD THE CORE!" flashes on-screen, simply do as it says and press A once.
Watch as Samus dumps a massive stream of Phazon energy right into the core's largest eye. She then returns to normal and lands on the ground, nonchalantly leaving the chamber as the core writhes before literally erupting in a burst of its own juices. With that, Samus quickly exits the Leviathan aboard her gunship - watch as the entire structure cascadingly explodes, saving Bryyo and bringing you one step closer to victory.
Samus leaves Bryyo and enters low orbit before opening a channel with Aurora 242. After a quick thanks from the supercomputer, 242 explains your next target: Elysia. The planet where Ghor was stationed, Phazon corruption is still spreading throughout the planet. But unlike Bryyo, the Leviathan is embedded deep under turbulent storm clouds, so ground recon isn't possible. Instead, you'll be taking a trip to SkyTown - a Chozo-built facility high above the clouds where another Aurora Unit (217) is stationed.
Aurora 217 has naturally been infected by the Space Pirate's virus, so your first objective will be to bring it back online (242 grants your suit a vaccine to use, pity it doesn't work work on Samus herself). Once you're clear to leave take a moment to check on Samus' condition (strange that 242 didn't mention anything about it). Use the biohazard scan to learn that Samus' Phazon corruption level has now climbed to 25% - you'll also notice the stronger blue tinge to her suit, and switch on the Scan Visor and look up into space. Corruption is now showing on Samus' face, with her left eye's pupil turning slightly blue and a nasty Phazon vein cluster running up her nose (poor thing).