A small team of Shinra operatives have been sent to investigate the sudden spike in monster activity around the Nibelheim reactor. The Great General Sephiroth, SOLDIER 1st Class Zack Fair, and two grunts (one of which is Cloud Strife) make up the investigative team. Due to the time zone change, no one can sleep. Zack convinces Cloud to tell a ghost story, and Cloud tells them about the rumors concerning the Shinra mansion. Intrigued, Sephiroth orders they investigate immediately. They discover a man locked in a coffin inside the mansion's crypt still very much alive. The boys take him with them, and Vincent tells them what really happened twenty-six years ago in Nibelheim. Because of Vincent's insight into what happened, Sephiroth avoids his canonical Start of Darkness and the plot takes a sharp left turn away from canon events.
The boys return to Midgar with Vincent and Tifa in tow. Sephiroth begins to suspect that not only is Shinra keeping him in the dark, they are intentionally manipulating him and he doesn't like it. Vincent provides him with excuses for leaving the Shinra building more often than usual, and Veld and the Turks rescue information about Sephiroth's past that might have otherwise been destroyed. Although he now has a lot of information about his past, Sephiroth still has few answers. A resurgence by Avalanche provides him with an excuse to leave Midgar and take what's left of the army with him.
Deepground Interlude I
We see what has become of Rosso, and how her handlers respond to her failure. Nero attempts to help, but winds up complicating the situation which results in both of them being punished. The Restrictors- four black-clad beings who rule Deepground- oversee their punishment personally. Nero is made to try to breathe without his respirator, and Rosso is forced to watch as he suffocates. Later Weiss- who is ignorant of what happened- asks Rosso if he can sleep with her. Used to such requests, Rosso agrees. This particular encounter goes a bit differently than those previous. Rosso, who cannot feel pain, is usually indifferent to intercourse and only indulges Weiss because she knows he enjoys it. This time, however, Rosso is able to experience pleasure. All three of them end up passing an enjoyable evening together.
Act Two - Corel
Rufus Shinra is trying to talk Corel into a makou reactor, and so far it's been a hard sell. Sephiroth arrives and shares his findings with Rufus, who agrees that he doesn't like where the company is headed. He, Sephiroth, and the Shinra personnel that had come with them essentially announce a hostile takeover of the company, vowing- among other things- to halt any further production of makou reactors.
Avalanche arrives, and rather than fight them, Sephiroth offers Elfe a truce. At first she wants to duel with him, but then cautiously accepts. Not long after, President Shinra Sr. retaliates by sending Deepground troops after his AWOL staff. SOLDIER, Shinra, the Turks, and Avalanche must work together to defeat their common enemy. They capture Azul the Cerulean in the process. Azul surrenders willingly on the condition that they help him free his family from Deepground.
Deepground Interlude II
Weiss is scheduled for his turn in the Deepground Breeding Program. Deepground captures people no one will miss from the surface, and forces them into service. All women of child-bearing age are forced to sleep with various men in order to create the next generation of SOLDIERS. Because of his recent experience with Rosso, Weiss does his best to be kind and to make sure that his partner enjoys the experience as much as she can, given the circumstances. His partner- whom he refers to as "Jane"- is grateful and teaches him a few bad habits.
Act Three - Corel Continued
Afraid that a second wave is not far behind, Sephiroth, Elfe, Vincent, and Zack head to Corel Prison for additional troops at Azul's suggestion. On the way, they run into Genesis, who is not as dead as everyone thought. Like Elfe, he wants to fight, but Sephiroth refuses to engage him. They hug it out, and the two of them chat a bit about their respective origins.
The party returns successfully from the prison to find disaster has struck Corel. The corpses of the Deepground soldiers aren't turning to pyreflies, but are instead lying around rotting. As a result, several people come down with a mysterious illness. Vincent recognizes it as Geostigma. They aren't given much time to consider this new wrinkle, as Jenova herself appears, reanimating the corpses of the Deepground soldiers and seizing control of any living SOLDIERS. The Turks, the regular army, and anyone else who thinks they can help engage the possessed troops. Aeris summons her Healing Rain, washing away the worst of Jenova, and forcing the alien parasite to retreat. Chaos tries to finish her off, but Jenova swallows him whole before escaping over the side of a cliff.
The battle won, the team takes stock. While it could have been worse, there are a number of new developments. Chief among them, Sephiroth has gained his wing, and Elfe has come down with Geostigma. Although Aeris' Healing Rain has cleansed the SOLDIERS and many of the human Deepground troops (who then defect to serve under Azul, adding to Shinra/Avalanche's numbers), it has proven dangerous to those born with Jenova's DNA. If Sephiroth and Genesis hope to be free of Jenova's influence, the must find another remedy. Elfe likewise needs a different cure. The Healing Rain water is not enough. If she is to survive, she needs the two additional fragments of the Zirconiade materia. Lazard has one, and Sephiroth has a guess as to who holds the final piece.
Deepground Interlude III
Weiss does some soul-searching. He comes to the conclusion that he no longer wants to participate in the Breeding Program, and shares this with Nero. Nero doesn't really get it, but agrees to help Weiss track down Jane as Weiss wishes to speak with her. The two of them infiltrate the forbidden area where the Mothers and children are kept. Weiss apologizes to Jane and offers to keep her safe. Nero uses his shadows to secret her to the dark mako caverns where she will not have to suffer the advances of anyone else.
Act Four - Limbo
Vincent has survived his fight with Jenova, and finds himself in the crystal cavern where Lucrecia and his father originally found Chaos. He discovers Lucrecia there, her body preserved in a hollow spear of materia. Chaos persuades Vincent that if he tears the materia out of his body, his soul will be able to rest and rejoin the Lifestream, and Chaos will be free to defeat Jenova. Vincent agrees and tears the Chaos materia out of his chest. This separates Vincent and his headmates, but they are not able to rejoin the Planet. Vincent encounters Lucrecia, and the two of them are able to sort out a few things. Lucrecia senses that Sephiroth is in trouble- she is able to see through his eyes when he is in pain or in trouble- and Vincent volunteers to help. He, Chaos, Galian, Gigas, and Masuka agree to reunite in order to save Sephiroth and defeat Jenova. Vincent promises Lucrecia he will come back to her before returning to the waking world.
Sephiroth, Azul, Reno, Rude, and Elena infiltrate Midgar using the same empty mako aquifers that the Deepground troops had used to traverse the ocean. Lazard happily surrenders his Zirconiade shard to Sephiroth and offers some additional details as to what Shinra has been up to. The Shinra board is on Sephiroth's side, but is limited in what they can do to help him. Palmer and Scarlet steal Sephiroth's younger brothers (the Remnants of "Advent Children") so that they will not be added to the ranks of Deepground. Palmer's family offers to take care of them until things calm down. Sephiroth sends the Turks with them to guard them and infiltrates the Shinra building himself. There he confronts Professor Hojo and narrowly escapes Hojo/Jenova's clutches thanks to Vincent, who is not as dead as everyone thought.
Sephiroth gives the remaining Zirconiade shards to Elfe, which heals her instantly. Zirconiade appears to Sephiroth and thanks him for his aid. Sephiroth asks that Zirconiade kill him if he should lose his senses to Jenova again and she reluctantly agrees. Zirconiade vanishes, and Elfe and Sephiroth talk about their memories of Hojo. Although Sephiroth did not like Hojo, he was still a huge part of his life, and has left a bigger hole than he had anticipated. Elfe is grateful for what Sephiroth has done and does her best to comfort him.
Genesis gives Elfe something of a [1]. While he does not threaten her should she break his best friend's heart, he does present the various hazards of entering into a relationship with someone like Sephiroth. He wants to know is she is committed. Elfe is unable to answer, as Sephiroth himself interrupts their friendly duel. Genesis departs and Elfe and Sephiroth duel for a bit. It results in them sharing a [2]. Although this has been a long time in coming, both agree that now is not the time for romance. Should things go well, they will attempt pursuing a relationship once Jenova is gone.
Deepground Interlude IV
The Tsviets are unable to keep Jane from dying of Mother's Disease (their name for Geostigma). She asks that Weiss put an end to her suffering, and he agrees, breaking her neck. Jane's death has a deep effect on Weiss, Rosso, and Nero. All three of them have learned "bad habits" from her that include love, and displays of affection. The Restrictors catch Weiss and Rosso kissing and confessing their feelings to one another. To punish Rosso, they leave Nero to suffocate. To punish Weiss, they brutalize Rosso so that she will be undesirable to Weiss as a sexual partner. After that, they are separated. Weiss- assuming Nero has died and that Rosso hates him- is ready to give up until his troops arrive to take care of him and beg for his protection. Weiss reluctantly agrees.
Act Five - Final Boss Battle
[Big Badass Battle Sequence] in which the joint forces of Shinra and Avalanche invade Midgar. Elfe and Zack lead the charge while Sephiroth and Genesis hang back, afraid that they will lose their senses to Jenova if they attempt to join the fray. The Shinra board has commandeered some additional help by stealing some Gelnikas and the Highwind airship. Sephiroth and Genesis are able to command from above aboard the Highwind while keeping an eye on the battle.
While the battle rages above ground, Vincent infiltrates Deepground to shut down the mainframe that controls the microchips in the bodies of the Deepground soldiers. Before he can complete his task, Jenova punches through the bedrock and the Shinra building ala Godzilla. Sephiroth and Genesis immediately lose control to her.
Aeris has been under guard at the extreme rear of the Shinra/Avalanche forces for her own safety. She now ventures into Midgar to summon Holy (in the form of various ghosts who rise up out of the light mako beneath Midgar) and an encore of her Healing Rain. Holy protects the Midgar citizens from harm and help to keep the Plate from crushing anyone. The Healing Rain cleanses or kills those affected by Jenova. With help from the Guardian Summons- Chaos, Zirconiade, Alpha, and Omega- Jenova is vanquished. Because of the Healing Rain, Sephiroth, Genesis, and the Tsviets are in bad shape. It is Vincent's idea to implant Holy in Sephiroth's body. Aeris asks the Shinra/Avalanche troops for additional Summon materia to save Genesis and the Tsviets. Their impromptu field medicine is successful. Sephiroth and Genesis now have two wings instead of just one.
Epilogue
Sephiroth awakes some time later in a field hospital. Elfe has been sitting with him. She assures him that they were victorious and that everyone he cares about is safe. They kiss and spend some time together. Now they are free to pursue their own feelings and a new life without Jenova.
