In Makai, Alice defeats Mai, though she still doesn't forgive her. Keeping her promise, Shinki sends Alice and Sakuya back to Yumei's Gensokyo, with a warning regarding what was prophesized to kill Alice: A beast with green eyes. When they return, they find themselves in a densely grown forest.
In Gensokyo's subterrain, Marisa and Youmu wake up, only to discover that Reimu has gone missing, and a note from her, saying that she had gone to "find something out" and that she'll catch up later. Marisa insists on looking for Reimu, but Youmu points out that Reimu left no leads in which to follow her, so the two of them reluctantly go on ahead, and eventually exit the subterrain to elsewhere in the same forest Alice and Sakuya had returned to.
In the ruined city, Mokou and Cirno's relationship grows and Mokou reveals her plans to wander whatever the world becomes when everything is over, and if Cirno would want to be her companion. Cirno accepts. However, they are soon attacked by a giant robot piloted by Nitori. Mokou, Cirno, Reisen, and Yuyuko make a run for it to a highway, where they find a car that miraculously still works. A second chase ensues with Reisen at the wheel. It ends where they find a ruined part of the highway, which they use as a ramp to launch their car at Nitori. They bail out as it crashes and Mokou ignites the fuel tank, blowing it up and destroying the machine (Nitori's fate is left unknown). They go on.
Reimu, haunted by what Yumei had told her, goes to Satori, looking for answers. Satori uses the technique she used to fight Youmu, and Reimu encounters her inner self (the "white" Reimu).
Mokou, Cirno, Reisen, and Yuyuko reach the outskirts of the city and a wasteland stretches before them. At that moment, they are attacked by Suika and Yuugi. The two oni prove to be too powerful for them, and Yuyuko, as a last resort, uses her Last Word to defeat them. As a result, Yuyuko, whose energy had reaches zero, disappears from Yumei's Gensokyo and find her weakened self back in Hakugyokurou. She is encountered by Mima, who suddenly betrays and imprisons her, and then proceeds to take over.
In the other Netherworld (the one Yukari was sent to), Toyohime, for secret reasons, releases Yukari, Sikieiki, and Komachi, returns Komachi's scythe, and allows them one chance to try to escape. With two objectives, finding a way to remove the energy-suppressing rings, and finding Kotohime and getting Yukari's power back, they set out. However, their progress is slow, due to only Komachi having the power to fight, and they have to go unseen.
Parsee borrows a photograph from Aya, of Marisa and Alice sharing a moment, and then shows it to Flandre (who has a hopeless crush on Marisa) as fuel for her jealousy manipulation (under Parsee's influence, Flandre's eyes turn green, if you want to take an early guess on where I'm going with this...)
At the Moriya Shrine, where Kaguya and Eirin were being held captive, Sanae disobeys instuctions not to feed them anything, nice girl that she is. Eirin takes advantage of this and frees herself and Kaguya. On their way out, they are encountered by Kanako and Suwako, but with Sanae as a hostage, Eirin successfully negotiates with them into letting her and Kaguya escape.
In the forest, Alice and Sakuya are attacked by an irate Flandre, who proves to be too strong for them. Marisa and Youmu arrive just as Flandre morally wounds Alice, unable to change fate. Greatly angered, Marisa fires a Master Spark at the overhead growth, letting a sunbeam shine down, which Flandre gets caught in, killing her. Alice tearfully expresses her gratitude in getting to see Marisa one last time before she dies. Sakuya is upset over both Alice and Flandre's death, but Marisa is optimistic that they might be able to bring them back if they settle things with Yumei. Sakuya rejoins Marisa and Youmu, and they press on, and eventually see a tower over the horizon, approaching it to see if that's Yumei's stronghold.
The wasteland Mokou, Cirno, and Reisen are traveling through suddenly becomes a field of sunflowers, and they are attacked by Yuka. Yuka detains Mokou and Reisen, only interested in fighting Cirno (who, through a sheer stroke of luck, defeated her during the events of PoFV). Cirno is no match for Yuka, and she gets morally wounded. With her last breath, Cirno uses her Last Word, which cripples Yuka. Furious, Mokou breaks free of her binds, and ruthlessly and brutally finishes of Yuka. Reisen goes ahead, which Mokou stays behind for a few minutes to dig a grave for Cirno.
In the Netherworld, Yukari, Sikieiki, and Komachi find the controls for the rings and regain their ability to use energy attacks. They storm the detention complex, looking for Kotohime.
During the night, Marisa is encountered by Yumei, who tells her what she told Reimu back in the subterrain: Even if they succeed, only one world, Earth or Gensokyo, can be revived. Yumei leaves and Marisa is torn about what to do. She Master Sparks a hole in the ground and visits Satori, who allows Marisa to encounter her other self, and help her come to an answer.
Yukari, Sikieiki, and Komachi confront Kotohime, who is unfamiliar with how to use Yukari's powers, and the battle ends with Komachi cutting a large scar into the Lunarian princess' body, and a crystal flies out. Yukari touches it and regains her power of boundary manipulation. Leaving Kotohime for dead, they leave for Hakugyokurou. Afterward, Toyohime kills Kotohime, saying that a bright future for the Lunarians is only possible through her death. Kotohime, now a ghost, is encountered by the Yama she was bullying earlier, who promises to be a harsh judge.
Yukari, Sikieiki, and Komachi arrive in Hakugyokurou, only to find out from the Prismriver sisters that it had been taken over by Mima, and Yuyuko was imprisoned. Angered, Yukari swears she will make Mima pay.
One day passes and the night of a full moon approaches.
Yukari, Sikieiki, and Komachi confront Mima, and after a difficult battle defeat her. Yuyuko is freed and Mima is banished from Hakugyokurou.
Mokou and Reisen meet up with Eirin and Kaguya, at which point, they are attacked by Yumei, who summons a giant monster from the ground. They defeat Yumei who escapes afterward.
With the full moon high in the air, Marisa, Youmu, and Sakuya reach the tower, but at that moment, Meira, the current student of Youmu's father, appears, demanding a one-on-one match with Youmu, who accepts, while Marisa and Sakuya go ahead. The duel ends in a draw and Meira wonders before leaving who Youki had such a high opinion of Youmu.
Halfway up the tower, Marisa and Sakuya encounter Remilia, who is furious about what happened to Flandre. The mistress and servant fight while Marisa goes ahead. Sakuya barely wins by knocking out Remilia.
On top of the tower, where Yumei has retreated to after losing to Mokou and the others, she is encountered by Yumemi, the one who had made her into an experiment. The scientist expresses fascination, but Yumei is furious and attacks Yumemi. Yumemi is too powerful, however, and Yumei gets morally wounded as Marisa arrives. Marisa fights Yumemi, but she too is no match for the Lunarian scientist's psychokinetic powers. Understanding that Marisa was half of the reason the Yumei experiment was a success, she just takes a handful of Marisa's hair and leaves, excited to see what will happen when Yumei, the creator of the combined Earth/Gensokyo, dies.
Sakuya and Youmu catch up. Yumei is regretful that she couldn't get her revenge on Yumemi, but with her final breath, she releases the last of the energy she was infused with as a floating orb, saying that if Marisa or Reimu touches it, the world will be reformed to whatever they desire, and that she's doing that final deed out of thanks to Marisa and Reimu for being there when she was about to fade, even though it was an accident in actuality.
Yumei dies, and the land starts to shake, threatening to vanish. As Marisa is about to touch the orb, Reimu appears, asking which world Marisa had decided on. Marisa answers that she chose Earth, and Reimu says that she won't let Marisa do it, because she chose Gensokyo. Youmu and Sakuya both pick a side to support.
The final battle begins, with Marisa and Youmu, choosing Earth and reality, against Reimu and Sakuya, who choose Gensokyo and dreams. The battle ends with Reimu and Marisa making a desperate final dash for the orb, and they end up touching it at the same time.
Marisa and Reimu find themselves within their consciences, encountering their other selves, learning that both worlds can be returned, but they must sacrifice one of their halves to generate the energy to make it happen. Reimu sacrifices her Kiribayashi half, which Marisa discards her Kirisame half.
Both Earth and Gensokyo are returned to the way they were, with Gensokyo now as its own independent realm, only Marisa never existed within Gensokyo, while on Earth, Reimu Kiribayashi was never born. With the revival of Gensokyo, Yukari, Cirno, Alice, Flandre, and everyone else have returned to life. In Gensokyo, life returns to normal, like nothing had happened, while on Earth, Marisa, while sure she did the right thing, still thinks about Gensokyo and can?t even dream about it again, no matter how hard she tries. However, Yukari comes along from time to time to tell Marisa about what?s happening in Gensokyo, though the new laws governing the two realms prevent Marisa from coming with Yukari to Gensokyo and vice versa in Reimu?s case.
Epilogue:
On the moon, Youki Konpaku encounters the empress, who is deeply in grief over the death of Kotohime. He offers to end her misery and kills her (the empress is only immortal when she has a desire to live). With Youmu?s father having ended the life of Kaguya?s mother, the laws of Lunarian royalty dictate that anyone who proves to be strong and clever enough to kill the previous ruler is crowned the new emperor. This was all planned by Youki and Toyohime. Both Yorihime and Meira are less than thrilled about it.
On the night of a full moon in Gensokyo, the banished Mima happens across a blonde girl in black, who only recalls her name as being Marisa Kirisame. Mima takes the girl under her wing.