"In the year 20X9 of the Cosmic Calendar...
The galaxy is at peace. Galactic bounty hunter, Samus Aran, had successfully purged the galaxy of all Metroids, and even the parasitic organisms they fed on. The Space Pirates, once worthy of fear across space, have been reduced to just a few individuals, and even they have began to fall. Samus, having completed her goal of revenge against the Space Pirates and even the Metroids, has taken up the offer of leaving to explore the vastness of space for the Galactic Federation.
Tragedy strikes, however, when a large Galactic trade ship is destroyed by marauders, causing tens of thousands to die. These mauraders, initially thought to be the Space Pirates returning, are confirmed to be an entirely new group. After they make another strike on the Galactic Federation homeworld, all resources are set to track them down.
No one expected what would come next.
Galactic scouts track the mauraders back to FDS1986, a long abandoned planet, or so it seemed. Energy signals from within show that it is clearly alive, perhaps a giant piece of machinery, or something even worse. The Federation Force is not equipped for this type of dangerous exploratory mission.
Fearing a lack of manpower, the Galactic Federation calls in Samus Aran one last time to help them tackle the threat.
Samus Aran... Please help protect the galaxy once again. We're counting on you."
Approaching an oddly shaped planet in her gunship, Samus begins to recount her current mission. The Galactic Federation has known about the existence of this celestial body since the Federation was formed, but ancient regulations barred its officers from doing an investigation. The only thing they know is that its surface is biological, and that it is so dangerous that merely approaching it would have galaxy-wide implications. Unfortunately, multiple Federation vessels have recently been hijacked by beings that may have established a base on the body. The Federation has decided that, as contact has already been made there, the danger is likely overstated, and so Samus has been given the duty of surveying the planet for the first time while also taking down the maurauders there.
While she enters orbit around the planet, a large section of it begins to move, uncovering a gigantic eyeball. It slowly glows yellow, before shooting a tractor beam at her ship that she cannot escape. It captures the ship and keeps it still while bringing the ship closer to the eye. As it does so, the ship's lights flash on and off, and Samus goes unconsious while desperately mashing at the controls.
After the screen returns from a fade to black, Samus has crash landed somewhere inside the planet, with a dark sky above indicating that she is underground. Her gunship is nearby, completely decimated, and her suit is malfunctioning. She exits the suit in her Zero Suit and begins exploring. Although she finds no living organisms, she does find half-organic, half-mechanical objects that attack her, apparently a defense system, as well as numerous ruins suggesting a civilization once lived here.
After some discovery, Samus finds a sparkling being that runs away from her. She can track it to an underground area, where the being starts to shake and release electricity before turning into her Power Suit. She reluctantly puts it on, revealing it to be entirely intact, other than missing some upgrades. As she puts it on, it quickly transforms between various looks from her past, before settling on a new look. Going further into the room allows her to unlock the first map, one of the area called Ikoria she is in. A screen in the back of the room also shows flickering images of a large brain.
Eventually Samus can make her way through Ikoria to a large building that seems to lead to another area. Inside, a deranged being resembling a Space Pirate attacks her, and she realizes that it fits the description of the mauraders she was supposed to destroy. After taking care of it, it has a brief moment of consiousness, telling Samus through a translater the following:
"We made a mistake. We provoked the Brain, and now it provoked us. Destroy it for the good of all. No longer do we control. The body of Leviathan holds the entrance. Follow the cords to repeat out mistake and finish it"
Disturbed but determined, Samus continues onwards through the building, passing through a giant set of teeth and seeing a large, cavernous area resembling the mouth of a fish, where her journey begins.
After continuing to make progress throughout areas like the Mouth, the Stomach, and Heloz, Samus will inevitably find herself in the Hanging City, a giant city constructed out of bones and other biological matter. It is filled with dangerous robotic sentries and large turrets. Most notably, the background of the entire City holds three giant wires leading to a central spire. Reaching the spire and exploring it will reveal a large cannon pointed upwards.
By finding the various Logs in the area, Samus can discover that the Mouth has four large sunpanels in the ceiling that provide light for the entire body, allowing other things to live inside. The creators of the Hanging City built large harvestors to extract this energy directly, which was more efficient. Eventually, an uprising in the Hanging City lead to a new leader, who decided to reverse the direction of one of the harvestors to shoot their accumulated energy at the roof of the 8mouth, opening a path to the brain, which they went on to destroy.
In addition this reveltation, Samus can also find the Charge Capacitor here by defeating the boss, an animated statue of said leader. This upgrade allows her to defeat the boss of the Lung and finally enter the Heart, a pitch black area with a constant, slow beating and no other music. At the center of the area, Samus finds the titular body part, taken over by dark energy. Using her weapons, Samus can free the heart, opening bloodflow back to the body and thus allowing her to access the rest of the areas in the game.
As hinted at by the Hanging Garden Logs, the only way for Samus to find the Brain is to repower the cannon. The three wires of the Hanging City connected to the roof of the mouth at various large lights, which each had cords going from them to other body parts. Trailing these cords leads Samus to the three bosses she needs to defeat to restore power: the ones at the Eyes, the Fin, and Snaev. Getting to these three areas also involves Samus unlocking and using the new Exo-Suits mechanic. Logs in Varma reveal that the Exo-Suits, along with Varma's defense force, were built to allow the inhabitants of the beast.
Finally, Samus activates the three lights in the Mouth, and returns to the Hanging City, where the Cannon has been powered on again, along with the entire city, which is now much more dangerous. Turrets and sentries at full energy can deal lethal damage in just one hit. Samus must also fight the guardian statue once again before activating the cannon and opening her way up into the Brain to finish the job. After proceeding through dangerous rooms with hazards from many prevous areas, Samus finally finds the cranial room, occupied by hundreds of beings like the maurauder she saw before.
They come together and form into one giant being, which then attaches the brain to its head, resembling the final boss of Super Metroid. Samus must defeat the boss while also avoiding detaching maurauders. Once she finally does so, the brain lets out one last blast before falling off of the maurauders, causing them to begin to disintegrate.
Samus is now left alone in the cranial room, with loud warning sounds erupting around her. The door to leave opens. If she does not leave, she can find large glowng weak spots all over the brain stem, which can be shot with missiles to deal damage to the brain. If she manages to strike all the weak spots, the brain will be destroyed, killing the Leviathan forever. As Samus escapes the Leviathan on the rescue ship, she describes her experience, and her performance is reviewed. After showing her completion percentage for all the items collected, a cutscene begins, showing the ship flying away to a Galactic Federation outpost.
If Samus destroyed the brain, she is congratulated for finally ending the menace of the Leviathan. As the entire outpost celebrates with a large party, Samus is morose, mourning the loss of a large habitat and all those that lived on it for millenia, wondering if there was any alternative. If Samus did not destroy the brain, however, she is instead chastized for allowing the Leviathan to continue living as it has now blocked off entrance to its cranial room. However, if Samus collected all twelve Log Entries in the Leviathan, she can respond with an idea: by expanding the solar panel and refrigeration systems, the Galactic Federation can ensure that the Leviathan will never have to eat another planet, while also giving a way for them to control it for use in galactic peacekeeping. A final cutscene shows the contruction efforts at the Leviathan, ending with the Leviathan taking part in training with the Galactic navy. Samus gives a thumsb up to it before heading off in her repaired gunship.