Rini falls ill and the Luna-ball floats up and is replaced by an image of another scout, who is introduced as Sailor Pluto. Pluto tells them that Rini is being attacked in her dreams. The scouts enter Rini's dreams and get their first glimpse of Crystal Tokyo of the future. It is a ruined, desolate place. At first Rini doesn't know who Sailor Moon is but later remembers. They defeat a droid that looks like the Grim Reaper, and Rini is healed when she dreams of saving her mother.
Meanwhile, Esmeraude has taken over for Rubeus and tells Prince Demand in the future that instead of taking over crystal points, she will open a Black Gate that will obliterate life on Earth so that in the future, they can easily take over the planet. With the help of Saffir's crystal figurines, Esmeraude must place them in key areas to become dark points for the Black Gate to open up. When the figurine has grown enough, a droid will appear to guard it. Of course, Sailor Moon and the scouts always thwart her at each point. (These episodes turn into the regular villain captures point, droid appears and guards it, scouts stumble on it, defeat droid, villain appears swearing revenge. One episode is extremely funny. Esmeraude has made everyone at Christmas catch a flu virus except Mina. With Artemis she goes around to the others to help them get better, except her accident-prone nature has caused more problems than soothe. At Raye's house, she fiddles with her tape player before it explodes. A scorched-Mina blinks in surprise.)
Now, the moment we've all be waiting for. During one of these episodes (with Esmeraude taking over places) Serena has the same dream Darien's been having. She sees herself at her wedding and afterwards, her floating away while everything around her is being destroyed. She awakens and looks at a picture of her and Darien together and suddenly the glass shatters! She goes to his apartment and tells Darien of the dream. They talk for a bit, but Darien is starting to believe it is real and pushes her out of the apartment. Serena cries at the door that even if the world were destroyed she'd still want to be with him. Later in that episode, Tuxedo Mask shows up and says that he is willing to fight alongside them and tells Sailor Moon it is their duty to protect Rini and in essence, protect the future. He leaves, but Sailor Mars urges Serena to follow him. They meet in a secluded place where Darien waits. They embrace and kiss, finally back together.
Rini has decided that she wants to go back to the future because she's found Sailor Moon and feel they can help her mother. She takes them to the gateway between times where Sailor Pluto is the guardian of time. They emerge in Crystal Tokyo, and just like in Rini's dream, it is absolutely dark and destroyed place. Rini runs off at the sight of the place. They look for her when a ghostly apparition appears. He introduces himself as King Endymion. The scouts notice he looks exactly like Tuxedo Mask. He says he is Darien, of the future. Tuxedo Mask realizes that his voice was the same as the voice in his dreams and sees a trap. He attacks but he cannot hit the image. King Endymion admits he sent those nightmares as a test. He had to know that their love would stand up against that nightmare because they were destined to face even greater challenges. He takes them to the Crystal Palace.
There, he tells them the story of Crystal Tokyo. In the past, a great catastrophe frozen all of Earth's people. They were frozen until the 30th Century when (somehow) Neo-Queen Serenity (Serena) used the Silver Crystal to free them and they created the paradise of Crystal Tokyo. However, some people were opposed to Serena as their Queen and they rebelled. With King Endymion by her side, they banished the rebels to a distant moon. On that moon, an evil force (Dark Nemesis) corrupted the people and their hatred for Earth grew until the Dark Moon appeared, ready to conquer Earth for their own. Unexpectedly, the Silver Crystal disappeared and the Dark Moon attacked. Neo-Queen Serenity was outside and an energy blast hit her. The scouts of the future tried to protect her but couldn't and a crystal case grew around her and she fell into a deep sleep. King Endymion was injured too and was recovering, but hooked himself up to a computer and a hologram is what they are seeing. Meanwhile, the future scouts (whom we never meet closeup) are holding up the shield that is protecting them but they are growing weaker. Finally, King Endymion reveals that Rini is in fact Serena and Darien's daughter (Serena hadn't figured it out yet!) and their faces grow bright red. The other scouts began to realize similarities between Serena and Rini, except Raye, who demands to know when all this happened! (Remember, she used to date Darien!)
Meanwhile, Prince Demand in his nearby Dark Citadel has noticed Sailor Moon's arrival into the future. He pieces together Sailor Moon's resemblance to Neo-Queen Serenity and is entranced by her beauty. Several times he tries to capture her and force her to love him but Tuxedo Mask (quite mad!) rescues her.
When Sailor Moon tries to use her own Silver Crystal and fails, Rini becomes convinced not even Sailor Moon can save her mother. She runs off and leaves the safety of the shield. Outside the Wiseman paralyzes her and from her memories, we learn the reason of Neo-Queen Serenity's encasement in crystal. One day, Rini had accidentally broken a vase and the servants scolded her, saying she should be more graceful like her mother (seems Serena grew out her klutziness but transferred it to Rini!). Rini wanted so much to be like her mother that she went into the room holding the Silver Crystal. She held it up, hoping it would make her more graceful but instead it disappeared. She was afraid she would be really punished for this and ran off. Suddenly the Dark Moon began attacking. Neo-Queen Serenity went to look for Rini and was caught outside the safety of the palace. Rini kept saying she wasn't the reason for her mother's predicament when in her heart she believed she was. The Wiseman said he believed it wasn't her fault and tricked Rini into following him. He took her into the Dark Citadel where he began reviving memories when she was mad at people (eg. One time she was walking in the rain when she spotted a frog and went after it. Her mother said not to, and Rini fell. She cried and asked her mother to help her up, but she refused, saying that she should have listened. Rini looked to King Endymion but to her shock, he told her to listen to her mother and get up herself. She cried out she hated both of them.) From those kinds of memories, the Wiseman corrupted Rini and she transformed into Black Lady, a grown up version of Rini, with a dark inverted crescent moon on her forehead.
Esmeraude, jealous of Demand's attention for Sailor Moon demands to know her future. Wiseman tells her she will learn to control the Dark Crystal and be Queen of the Dark Moon beside Prince Demand. This is exactly what she wanted to hear, and Wiseman gives her a Black Crystal Tiara which transforms her, first into a beautiful queen, then as the dark energy surrounds her, a dragon. The dragon attacks Crystal Tokyo, but is eventually defeated. As the dragon falls to the ground, it turns back into Esmeraude who whispers Demand's name before she dies. The scouts are called back into the palace where an image of Sailor Pluto tells them something strange has happened to Rini and they must return to the past. Back in their time, the scouts notice a dark crystal growing larger and larger. They are about to approach it when Black Lady appears. When Luna-ball goes towards her and the moon on its face changes to the dark inverted crescent moon, Sailor Moon realizes that Black Lady is really Rini. They fight before Sailor Moon begins to heal Black Lady. She remembers when everyone seemingly forgot about her birthday when in fact they were holding a surprise party (typical!). (Note: The future scouts look the same as the scouts we know except their faces may be a little more mature and they have light lipstick) But the Wiseman counters it by feeding Black Lady more dark energy and she resists the transformation. He makes Black Lady think the memory of the party never happened.
Back in the future, Saffir, Demand's younger brother, learns that the Wiseman is using all of them to unleash the Dark Nemesis onto the world and destroy everything. A glimpse under his cowl briefly shows a skull! Saffir, realizing that Wiseman's goals weren't the same as theirs (ie, to take over Earth, not destroy everything!) he steals a key card and returns to the past, but not before Wiseman has injured him. He staggers around the streets before he passes out. He awakens in the apartment of the sisters and Prisma is taking care of him. He tells her of Wiseman's plans and that he must speak to Demand, whom he is sure will not hurt his brother. Prisma, obviously in love with Saffir urges him not to go, but she lets him leave. He leaves behind his coat which she hangs up on the wall. Katsy calls Serena and tells them of Saffir's plans. They meet at the crystal (now huge!) and protect Saffir. Black Lady manages to trap the scouts under a dome of energy but Saffir makes it to Demand who is willing to listen to what he has to say. Suddenly, a blast of energy hits Saffir and another, he dies. The Wiseman says he doesn't need permission to kill traitors and vanishes. Sailor Moon and Tuxedo Mask run to Saffir, and the bandage around his head loosens revealing the dark moon is no longer on his head. Demand takes his body and whispers Wiseman's name in rage. At the sister's apartment, Saffir's coat symbolically falls off the peg from the wall. Prisma clutches it and just after Saffir dies, his coat disappears. Prisma stands at the balcony, weeping.
Back in the future, Demand wants to know why he killed Saffir. Wiseman says he got in the way. Although Demand sort of knows Wiseman is using them, he still agrees that they will conquer Earth. But he promises afterwards he will find out the truth about his brother's death. Wiseman admits, after he leaves, that Demand won't live long enough. At the huge crystal, Sailor Moon and the scouts enter it using Sailor Teleport. There, Sailor Moon is separated from the others. She meets Demand who tries once more to hypnotize Sailor Moon into loving him. She resists eventually and that's when Wiseman appears saying he must kill her. Wiseman and Demand fight, equally matched, but when he attacks Sailor Moon, Demand takes the blow. Just before he dies, he gives his best shot and disperses the Wiseman, his cloak and ball fall to the ground. Demand realizes how much Wiseman deceived his people and the only hope for them lies in the sisters who now live as regular people. He dies, and Wiseman rises up and attacks Sailor Moon. He shows her images of Tuxedo Mask and Black Lady kissing and rejecting her, trying to trick Sailor Moon. She resists and Tuxedo Mask shows up with the scouts. Wiseman says they are too late, now that Black Lady's energy is at it's maximum and together they open the Black Gate.
Sailor Moon tries to heal Black Lady with the Silver Crystal, her attempt is so powerful, that in the future, Neo-Queen Serenity's body begins to glow. When the brightness stops, Sailor Moon is now dressed as Neo-Queen Serenity and she calls out for Rini to remember her past. (Really cool flashback, back with the Rini who fell and her parents refuse to help her. Neo-Queen Serenity explains that she wants Rini to grow up strong and able to depend on herself.) Wiseman engulfs Black Lady, Serena and Tuxedo Mask in dark power and they disappear. In a strange void, Black Lady is once more convinced everyone hates her. Serena tells her that isn't so, that she would give up her life to save Rini. She calls out for Rini and to remember all the good times. Black Lady begins remembering all the good times she had with the scouts in the past, and with Darien and Serena. Serena says that life is filled with bad times but that it is important to remember to good times and the people who love her. Finally, Black Lady embraces Serena and they emerge from the void, now Rini as herself, saying how sorry she was; Serena back as Sailor Moon.
Wiseman, shocked over the loss of Black Lady says it doesn't matter, that the Death Phantom and Dark Nemesis will emerge to destroy everything. Sailor Moon once more transforms into Neo-Queen Serenity and shouts "Moon Crystal Power" and challenges the Wiseman. His crystal ball lances out a dark beam and they collide. Serena is having difficulty holding her own. Rini cries into Tuxedo Mask's cape and when a tear hits the ground, it becomes another Silver Crystal. Then Rini realizes that the Silver Crystal she picked up from the future didn't disappear, but merged into herself. She decides to use her crystal to help Serena and she transforms into Small Lady, with a little dress like Serena's. The two of them float into the air, while on the ground, the scouts hold hands and their tiara's crystals grow, adding their power to the two in the air. Serena and Rini yell out for the Silver Crystal's to unite and a powerful beam overwhelms the Wiseman's beam and destroys him. The Black Gate closes and the crystal begins to shrink to nothingness.
Rini is on the docks, ready to return to the future. The scouts say goodbye but Serena is speechless, finally she and Rini embrace emotionally. Rini looks up and says, "Thank you... mama." She uses the time key and disappears into the future. Back in the future, Rini appears, and the world is once more beautiful. She races along the hills when she meets her parents and the future scouts. She stands and curtsies (how cute!) before she runs into Neo-Queen Serenity's arms and cries. The future scouts look on in happiness while Neo-Queen Serenity whispers, "Welcome home."