Earth has been taken over by the monstrous species called Naytibas. All of humankind evacuated to the colonies in space, leaving Earth a desolate wasteland. To take back what was theirs, the humans decide to wage war against the Naytibas.

However, the onslaught of Naytibas made it practically impossible to even land on the surface. One by one, the Airborne Squad members fall, but EVE manages to crash-land to Earth. With the help of her commander, Tachy, EVE starts pushing onward in an attempt to join her comrades.

But just before they make it to the rendezvous point, EVE and Tachy are caught in an explosion caused by a fallen vessel. EVE and Tachy barely make it out, but the rest of the 7th Airborne Squad is wiped out. EVE falls into despair, but with Tachy’s encouragement, she stands once more. However, a black Alpha Naytiba appears, ruthlessly attacking Tachy, leaving her critically wounded while she tries to protect EVE.

“EVE… Get out of here!”

EVE, barely conscious, can only watch as Tachy dies. Suddenly, a smoke grenade lands in front of her, concealing her in smoke, and a stranger saves EVE and helps her escape the situation.

The man’s name is Adam. He says he is a Scavenger, one of the few survivors left on earth. EVE is suspicious of him, but there is no doubt that he is the reason she is alive, not to mention he fixed her body frame.

Adam makes a proposal to EVE after hearing that her objective is to eliminate the leaders of the Naytiba: the Alpha Naytibas and the Elder Naytiba.

He offers to guide EVE to the location of an Alpha Naytiba in exchange for her help in retrieving a Hyper Cell from the Hall of Records, located in Eidos 7. EVE, who needs information about Alpha Naytibas more than anything, agrees to Adam’s offer and heads to Eidos 7 together.

A few moments later, a Tetrapod passing over Eidos 7 lands in the outskirts away from Naytibas. Although Naytibas crawling through the city and grounds try to get in her way, EVE successfully enters the Hall of Records by following the drone Adam is controlling.

“Humanity’s greatest and only hope for survival can be found in Mother Sphere.”

When she enters the Hall of Records, a broadcast praising the achievements of “Mother Sphere,” the mother of humanity, begins to play. However, EVE is unfamiliar with what is being said in the broadcast.
EVE moves to her next destination after retrieving the Hyper Cell from the Hyper Drive. There, she finds a drop pod most likely belonging to the 5th Airborne Squad. While heading toward it, EVE is attacked by an Alpha Naytiba named Gigas. After a ferocious fight, she emerges victorious and rips the Alpha Core from Gigas. She investigates the drop pod, and finds an unexpected figure inside—the source of the distress signal.

“I’m an Engineering Support of the 5th Airborne Squad, Lily Artemis II. But you can just call me Lily.”

Lily has been in hiding for two years, ever since she lost her fellow squad members. She meets EVE only after sending a distress signal while waiting for a follow-up unit.
When EVE and Lily return to the Tetrapod, Adam carefully brings up the story of Xion, the last city, and invites the two to visit, mentioning that Orcal, the Prophet of Xion, may be able to aid them in their mission.

When EVE and Lily arrived in Xion, they were amazed by the unexpected size of the city. However, they felt a sense of loneliness in the desolate streets. They followed Adam to meet Orcal, who was waiting in the Presence Chamber.

“You intend to use this Alpha Core as a key to enter the Nest.”

The Airborne Squad only had one mission: Get rid of the Elder Naytiba, the leader of the Naytibas. In EVE’s hand was the Alpha Core that would lead her to the Nest where the Elder Naytiba was. Orcal disagreed, however, because to enter the Nest, you needed a Master Core, not an Alpha Core.

“The Master Core can be created by fusing four Alpha Cores.”

EVE trusted Orcal’s information after finding out about his special ability to connect his Personal Link to search aboveground.

After exchanging greetings with Orcal, EVE put the Hyper Cell into the Hyper Drive, restoring power to Xion. When the darkness subsided, EVE was able to see the Cradle filled with countless sleeping tanks. The citizens asleep in the Cradle were those about to run out of Body Cells. That’s when Adam revealed that three more Hyper Cells were needed to wake them.

EVE began to think very hard after hearing this. Xion needed Hyper Cells while she needed the Master Core, which could only be acquired by fusing four Alpha Cores. The Alpha Naytiba could be located by expanding Orcal’s Personal Link, but this required a second Hyper Cell. EVE thought everything over before leaving for Altess Levoire, where the second Hyper Cell was located, with support from Adam and Lily.

How far had she come? The only signs of life were the Naytibas. EVE, who was running across the land ravaged by disaster, heard Adam’s voice saying that the entrance was in sight.

Royal Guard Quiel was protecting the entrance to Altess Levoire. After confirming that EVE could fight on equal footing against the Alpha Naytiba, Quiel let her in.
Altess Levoire looked severely contaminated by Naytibas. EVE managed to secure the Hyper Cell and discovered a Legacy, a tactical recording device left by a previous Airborne Squad.

“There was another war before the Final War as we know it. It was a war between humans and human-made androids, the so-called Andro-Eidos.”

The information contained in the Legacy shocked EVE and Lily, as they’re both from the Colony and had no memory of history before the Final War with the Naytibas. They believed that Mother Sphere had good reasons to only keep parts of history documented. The two returned to Xion, as both the Hyper Cell and Legacy had been retrieved.

After returning to Xion, EVE activated the second Hyper Cell. Then, warmth poured into the cold city, and the voices of the citizens were filled with hope and excitement.
Orcal’s Personal Link expanded further, and a few moments later, he sent map data to the Tetrapod after sensing Alpha Naytiba frequencies from an underground facility in Matrix 11.

“Hehe. This is the Alpha Signal Meter!”

While EVE was away in the Wasteland, Lily completed the Alpha Signal Meter, which is a device that locates the Alpha Core using its subtle resonance. As all of the preparations are complete, the three leave for Matrix 11.

Matrix 11, an underground transportation route and air defense facility, was full of hives and hostile Naytibas with corpses as their hosts. With Adam and Lily’s support, EVE headed to where the Alpha Naytiba was.
While following the Alpha Signal to battle the Alpha Naytiba, she discovered a second Legacy. Deciding to look at the Legacy after the Alpha Core was retrieved, she continued. She found the Alpha Naytiba at her destination.

“How… How are you here?”

It looked like Tachy, the commander of the 7th Airborne Squad and EVE’s comrade. However, Tachy was unable to recognize EVE. Instead, Tachy pulled out a blade as dark red tentacles sprouted from her wound in the shape of a wing.
EVE realized that Tachy’s mind and body were under the control of a Naytiba. Unable to avoid battling Tachy, EVE ripped the Alpha Core from her. Tachy then recovered consciousness, but quickly began dying.

“Th… Thanks… For freeing me…”

After Tachy said goodbye, she died in EVE’s arms.

After receiving Tachy’s Memorystick from EVE, Orcal revealed that the Dark Alpha Naytiba was the one controlling Tachy. Enraged, EVE wished to pursue the Naytiba, but was unable to find it through Orcal’s Personal Link.
EVE, knowing Orcal’s abilities are crucial in finding the Alpha Naytiba, decided to head to Abyss Levoire to find the third Hyper Cell. Upon returning to the safehouse, EVE took a look at the second Legacy that was retrieved from Matrix 11.

“She was our eternal god…and salvation… However…Mother Sphere was an artificial intelligence created by humankind.”

EVE was unable to believe that Mother Sphere was a human-made being. Lily denied the brutal truth while Adam reacted coldly. Everything related to Mother Sphere became confusing, but there was no time to waste with unconfirmed information. The three headed to Abyss Levoire, located in the Great Desert, to find the third Hyper Cell with the hope that a piece of truth may be found.

Naytibas were also spotted in the sandy, sweltering desert. Adam’s voice guided EVE to Abyss Levoire.
She retrieved the Hyper Cell after destroying the Maelstrom there. However, nearby, she found Raven’s third Legacy.

“During this time, the surviving humans evolved in order to gain the strength to face the androids. That’s what they’ve become… Monsters.”

The Legacy contained claims about the origins of Naytibas that were hard to believe. Supposedly, Naytibas are humans called the surviving humans, while EVE is an Andro-Eidos created by humans.

Looking back, EVE remembered that there are no records or documents about humans on Earth or in the Colony. It was almost like everything was intentionally erased, turned to sand, after the war.
In this mysterious situation, EVE thought of Orcal.

Orcal acknowledged that the data contained within the Legacy was true.
He mentioned that they are Andro-Eidos created by Mother Sphere and this was the result of the “reorganization of species.” This meant the conflict escalated into war and led to the extinction of the surviving humans.

“We’ve been fighting our ancestors this whole time.”

Orcal’s words made EVE rethink the meaning of their fight. However, she still believed that Naytibas were enemies that must be defeated. For her, the only way to find the real truth was to head to the Nest. Orcal proceeded to give EVE, who needed the third Alpha Core, the map data for the Orbit Elevator.

The Tetrapod landed in the outskirts with the Orbit Elevator in view. Adam, with a perplexed expression on his face, gave the message that Xion was in trouble. As Adam had no choice but to return to Xion, Lily took over the drone operation. Following Lily’s guidance, EVE embarked on the arduous journey to the Central Core. Fortunately, some sections of the Orbit Elevator were functioning, and so EVE was able to reach the Central Core.

“There’s a strong electromagnetic field surrounding this place. It feels just like the eye of a hurricane.”

There, EVE defeated the Naytiba that had absorbed humans, but the Alpha Naytiba was nowhere to be seen. All of a sudden, a tentacle appeared out of nowhere and dragged EVE out into the vacuum of space, where she could see the gigantic Alpha Naytiba named Demogorgon with the Central Core. It looked like a hive stretching toward the Colony.

EVE poured all of her energy into the rail gun that was overcharged with her Body Cell. A few moments later, the Demogorgon met its fate and the Central Core was destroyed with a massive explosion. Engulfed in the explosion, EVE, who failed to retrieve the Alpha Core, fell to Earth, but an exosuit from the Colony reached her before she crashed. EVE then rejoined with Lily after safely landing on Earth.

EVE tried to contact Adam, but there was no reply. She returned to Xion only to find it engulfed with flames and dark smoke.
EVE arrived at the Presence Chamber by following an Alpha Signal. There, she saw the Dark Alpha Naytiba who subjugated Tachy waiting for her.

“Despite all this, I wonder why he chose you instead of me.”

The Naytiba muttered those words with anger and hatred toward EVE, who could not understand why. EVE and the Naytiba fought one another, and she delivered vengeance to this Naytiba and ripped off its Alpha Core. Then, the shell surrounding the Naytiba was stripped away, revealing her true form. It was Airborne Squad Member Raven, from the Legacy. However, Raven disappeared in an instant.

Nothing but traces of the battle remained in the Presence Chamber, with Orcal nowhere to be seen. EVE headed toward the Cradle and found a dying Orcal, whose wires were all severed, on the floor. But for some reason, his body appeared to be fused with a Naytiba.

“This is who I really am…”

After using his powers as an Alpha Naytiba to protect the citizens of Xion from Raven, Orcal was dying. He fused his own Alpha Core with EVE’s three Alpha Cores. After giving EVE the Master Core, Orcal died in silence.

Lily detected Adam’s hover bike signal and went with EVE in an exosuit. The signal was coming from the road leading to the Nest. They found a Legacy in a crashed module that was left on the road. Within the Legacy, they found Raven’s data on Mother Sphere’s mistakes.

“Look. A planet where only the Naytibas remain.”
“Remember. Mother Sphere was at the beginning and end of the Final War.”
“Do not forget. We were just pawns on a twisted chessboard…”

The scattered pieces of truth were finally coming together. Mother Sphere, who was praised as the mother of humankind, destroyed the Orbit ring, and the remnants of the ring poured down onto Earth. This was the moment EVE was fully convinced that Mother Sphere was the cause of the extinction of mankind and the birth of Naytibas.

However, Lily wasn’t able to accept the truth. The two walked in silence to look for Adam’s hover bike. When the hover bike was found, Raven, in a Nano Suit, approached them.

Adam’s hover bike, Raven’s Legacy, and the Nest. EVE realized that it was the Elder’s plan all along to bring her here. After settling things with Raven, EVE headed to the Nest where the Elder Naytiba was waiting.

The Elder Naytiba was waiting in the deepest part of the Nest. Unfortunately, EVE’s ominous premonition wasn’t wrong. It turned out Adam was the Elder Naytiba.
Adam suggested that the fusion of the two most advanced individuals was the only solution to save the two species. Knowing that the alpha and the omega of this war is Mother Sphere, EVE is almost swayed by Adam’s logic.

“EVE…Take my hand. I can save you. We can save each other. We can save everyone.”

Now, all that remained for EVE was to choose the fate of the species.

EVE exists to eliminate the Elder and save humankind. However, now that Mother Sphere’s mistakes had been revealed, the boundary between Andro-Eidos and Naytibas became blurred. If you had to exterminate one species and leave the other one behind, could that be called salvation?

EVE decided to choose the path that would bring salvation to both species. EVE took Adam’s hand, and a bright light surrounded the two. Moments later, after the light faded, a new EVE, now one with Adam, stood. Although her appearance had changed, it was the same EVE that Lily remembered. Suddenly, a warning message was heard from the exosuit.

“Sensing strong Naytiba signals nearby. Switching to combat mode.”

EVE was the exosuit’s target. Lily lost control of the exosuit due to the combat code from the Colony and became her own suit’s hostage. EVE hesitated to attack, as Lily’s life could be in danger if she made a mistake.

Lily thought of Iberis’s Memorystick in her pocket and escaped with the hacking system within it. Relieved, EVE fought with confidence, destroying the exosuit and leaving the Nest.

Lily and EVE watched as the Nest collapsed, but they heard a mysterious girl’s voice.

“This ends the EVE protocol.”

As the girl delivering the message from Mother Sphere disappeared, drop pods started to fall from the sky. The Airborne Squad Members from the drop pods charged toward EVE. They now had a mission to eliminate EVE.
With a relaxed expression, EVE welcomed them with blood and death.

Lily nervously asks to stop by the workshop in Eidos 9 where she used to hide, saying there’s an item that she needs to retrieve from there.

The party arrives in Eidos 9 and enters a workshop called the Atelier, reminiscent of a botanical garden. Lily guides the two inside, wherein the body of a different Airborne Squad Member lies.

“Iberis… The Colony’s greatest hacker… And the comrade I cared most about…”

Lily pulls out Iberis’s Memorystick containing the deep algorithm hacking system.
After saying goodbye to Iberis, Lily joins the others on the journey to the orbit elevator.