As dark ghostly monsters loom at the bottom of the shaft, Haku recovers enough to fly again, and crashes into the boiler room through the ventilation shaft, on top of Kamaji. Even Kamaji realises that Haku has something wrong inside. Sen decides to feed Haku the herbal cake from the river god, and although he ahs a violent reaction, he vomits up a seal, and with it a little worm. The worm tries to escape, but the soot-sprites block the way. Sen stomps on it, smearing it all over her foot, but Kamaji performs a little cleansing ritual on her. Kamaji tells Sen that Zeniba's seal is that of a powerful witch. Haku reverts to human form, and Kamaji gives him a soothing brew while telling Sen of Haku's appearance at the bathhouse, wanting to learn sorcery from Yubaba, as he had nowhere left to go. However, Kamaji has noticed Haku's changing appearance over time, becoming paler yet with a sharp gleam in the eye. Meanwhile, the mouse and the soot-sprites re-enact Sen's heroic victory over the worm.

Sen tells Kamaji she wants to return Zeniba's seal and ask for her help in healing Haku. While Kamaji thinks getting there would be possible, returning is another matter. Lin enters and tells Sen of the goings-on upstairs, with Yubaba angry with Sen for allegedly letting the monster No-Face into the bathhouse. Sen admits this, although it was an honest mistake. Kamaji finds some train tickets in the bottom of his drawer, and tells Sen where to take the train to Zeniba's house. Although there is no return train, Sen resolves to walk back - but first, she must see about the unwelcome guest.

No-Face has been demanding to see Sen, and when she arrives, Yubaba angrily tells her to wheedle more gold out of the guest. She fails to recognise her son-turned-mouse, but there is no time for explanations as she shoves Sen into the guest's room. Sen encounters the grossly engorged No-Face, who offers her food, then gold, and finally pleads to know what she wants. But Sen tells him she has to leave, as he can't help her with what she wants, and that he should go, too. But this only disturbs him further, as he cries out his loneliness, and almost force-feeds his offered gold down Sen's throat. Her new-found mouse friend bites No-Face, and almost gets squashed for his trouble. Sen, fearing being eaten, offers No-Face the herbal cake she was saving for her parents. His gagging reaction to the cake is even more violent than Haku's and he flies after her in a rage. His fury is so great that even a spell from Yubaba doesn't stop him, and she gets covered in vomit instead. As No-Face crawls after Sen in an insectoid manner reminiscent of the cursed gods in Princess Mononoke, she leads him out of the bathhouse, temporarily halted along the way only by yet another wall at the bottom of a staircase. Lin is waiting in a punt outside, and Sen hops in, still drawing No-Face away from the bathhouse, which, she tells Lin, is the cause of his problems. Lin drops her off by the railway line, with a gruff parting from Lin. No-Face follows Sen, and receives a rather more threatening warning to not harm Sen.

Lin finds the platform, and the train arrives. The conductor counts out the tickets, noticing No-Face behind Sen. She decides to use up the final ticket for him, and they board the train which is occupied by rather shadowy, although human-like, figures. They find a spot to sit, and the serenity of the train's progress (and the accompanying background music) is contrasted with the childish glee with which Chihiro's mouse and bird friends embark on their ride. They pass various isolated places along the watery plain, stopping at stations to let passengers off until only the four remain, with Sen intently watching for their stop.

Back at the bathhouse, Haku awakes, and tells Kamaji that he heard Chihiro calling to him, and he followed her. From this, Kamaji realises the depth of Haku's love that he even knows Sen's true name. Yubaba is seething over the damage to the bathhouse wrought by No-Face in spite of the gold that he brought, and while railing at Sen for causing the mess, abandoning her work and her parents, tells her staff to slaughter Sen's parents for meat. Haku appears and asks Yubaba to reconsider, as she herself has not noticed the loss of something precious. She quickly examines the gold, but her "baby" is making distracting noises and she zips his lips. Her spell seems to react with the one cast by Zeniba, and the three green heads return to their original form. Added to this shocking development is the revelation that the gold produced by No-Face was only sand, and it crumbles before their eyes. Yubaba is in no mood to count costs though, as she frantically searches for her son. She flies at Haku in a rage, but when told that Bou is with Zeniba, Yubaba has the stuffing knocked out of her. Haku offers to bring Bou back, in exchange for the release of Sen and her parents. Yubaba decides to up the ante by threatening to do away with Haku after the deal is concluded.

Chihiro and her companions finally alight at their stop - a dark, deserted place with only one path. As they travel the path, the mosquito-bird tires from carrying Bou-mouse, so the Bou unselfishly decides to give the bird a ride on his back, spurning an offer to ride on Chihiro's shoulder. Greeted along the way by a hopping lantern (styled as a homage to the character Luxo Jr. produced by John Lasseter's Pixar), they are led to a country cottage where Zeniba invites them in, apparently expecting them. While Zeniba potters around and makes some tea, Chihiro urgently attends to her business by returning Zeniba's seal, and apologising on behalf of Haku. Zeniba is curious to know why Chihiro wasn't harmed while holding it, and Chihiro apologises for squashing the bug that was on the seal. Zeniba is amused, saying that the bug was put into Haku by Yubaba to control him. Chihiro asks Zeniba to change her little friends back, but she tells them the spell was long broken and they could change back if they wished. They decline, and instead have fun driving Zeniba's spinning wheel.

Over tea and cakes, Zeniba relates her differences with her vulgar twin, and says she can't help Chihiro with Haku or her parents, as that's for Chihiro alone. While Chihiro feels that she met Haku a long time ago, she asks Zeniba for some hint as to what she can do, but Zeniba mysteriously tells her that although she can't remember it, what happened is not forgotten. While Zeniba offers to put Chihiro up for the night and her companions help Zeniba with some good old-fashioned non-magical spinning and knitting, Chihiro grows ever more anxious to return, fearing for Haku and her parents. Zeniba gives her a hair band woven from the thread spun by her friends, telling her it will protect her. A rustle at the door alerts Zeniba to another guest. When Chihiro opens the door, she finds a white dragon with a green mane standing there. Chihiro rushes to embrace Haku, while Zeniba forgives him his actions under Yubaba's control. She bids farewell to the mosquito-bird and Bou-mouse, while No-Face stays on with Zeniba, having found his place at last. Chihiro tells Zeniba her real name, and is advised to take care of such a nice name.

Haku soars off with Chihiro and her friends into the moonlit sky, and as she once again grasps Haku's horns and peers out from between those wavy green strands of his mane, her memories well up again - of falling into green water, of a lost shoe, of the story her mother told her about an incident she can't remember, when she fell into a river when she was little. Although that river is now covered up, she remembers its name - the Kohaku River. That must be his real name - Kohaku. Instantly, the scales fall from Haku, and he appears to Chihiro as the boy she first saw. He tells her he remembers his real name - "Nigihayami Kohaku Nushi" - a name, Chihiro says, sounds like that of a god. He also remembers how Chihiro lost her shoe, and fell in, and she recalls how she was carried safely to shallow water. Tears of happiness and gratitude fly from Chihiro's eyes as they fall together through the sky.

As day breaks at the bathhouse, Yubaba paces in front of a selection of pigs. The staff excitedly point out Haku and Chihiro's return. Yubaba demands to see Bou, and is surprised when the mouse turns back into Bou before her eyes. She is even more surprised when she realises he is standing on his own two feet. Haku demands that Yubaba fulfil her side of the deal - but she has one more trick up her sleeve - she cannot break the spell unless the rules are followed. Despite the jeers of her staff and Bou's threat to be angry, Yubaba can't seem to do anything about it. Chihiro volunteers to take the test, which Haku has explained to her. She confidently marches across the bridge to Yubaba, who tells her to pick out her parents from the pigs in front of her. Chihiro is surprised that she can't find her parents at all among the pigs - which is the correct answer. Her contract turns to dust in Yubaba's hand, accompanied by the cheers of the staff.

Yubaba dismisses Chihiro, and Haku takes her hand as they head back to the riverbed - which is now dry once more. He warns her not to look back until safely back out of the tunnel. Although Haku cannot leave with Chihiro, his regained memory of his name will allow him to quit his apprenticeship and return to his own world, with the promise to Chihiro to meet again one day.

Chihiro hurries back down the hill to the empty train waiting room, where her parents are waiting impatiently. Surprised at this total ignorance of all that happened back there, Chihiro starts to look back - but remembers Haku's warning and turns away, her friends' protective hair-band glinting in the sun. Once again we see Chihiro clinging grimly to her mother as they walk through the dark tunnel. When they emerge back at the car, it is covered in leaves and dust as if left there for some time. Chihiro stares in wonderment back at the tunnel, as her parents call her to hurry. One last time, she turns away, her hair-band sparkling in the sun once more, and the tunnel recedes into the distance through the forest as they drive away.