Sayoran is confronted by one of the Clan Members and, knowing of Sakura's involvement, critizites him for having fallen in love and aided Sakura who, being a very inexperienced Magician, has broken the laws of magic by discovering the Clow Book without guidance and teachings of a mentor and has broken the law even further by creating her own Magical Cards.
Thus allowed someone as dangerous has Kaito to use her and Akiho, another illegal inexperienced Magican to steal Sakura's powers to use for a spell combined with the Watch and if the Sakura Cards are not restored or Sakura does not give up her powers, the world will be put into destruction and she will be punished.
Just as Sakura inadvertedly creates a 52nd Clear Card and capturing it, Yuna D.Kaito hypnotizes Akiho under his control and contronts Sakura who remembers that last time despite that Time has been re-written to save her life. Kero and Yue attempt to stop her from confronting Yuna and Akiho, but Kaito freezes them and puts them into a deep sleep with no awakening and does the same to Sakura's brother Toya and Sayoran so that no one will interfere. Sakura fails to stop Akiho who steals her Key and the Clear Cards before Kaito makes his appearence with Mono, thanking Sakura for her assistance and that now she must perish because he cannot allow her to stop him.
He reveals that, as she had foolishly believed that she didn't need to use the Sakura Cards or her original Star Key as no incidents had happened in two years, she inadvertedly erased all of the Clow
Cards to create her own as replacements, and that she had also foolishly fell in love since love is forbidden in the world of magic, thus he had no choice but to put her loved ones who had magic into deep sleep to prevent her from stopping him.
A guilt-ridden and grief-stricken Sakura weeps, especially when Kaito also tells her that all of the blame for everything that happened falls only onto her and uses Akiho to summon the dragon from Sakura's and Akiho's dreams to swallow Sakura whole before he shrinks it to the size of a tree and uses Akiho's book to absorb it and Sakura into it before removing it's magic, imprisoning her inside. Kaito then uses his magic to remove all memories of Sakura from the world to make it as though she never existed.
However, while imprisoned inside Akiho's "Alice in Clockland" Book and inside the stomach of the dragon, Sakura has another vision with Akiho who, seeing her face and gaining some control of her will, recongises her and asks what is going on, clearly unaware of Yuna's betrayal.
The regretful Sakura reveals what happened and that everything that happened was all her fault, wishing to have never discovered the Clow Book despite that she wouldn't have met or fell in love with Sayoran, but believes that it was probably best since she caused everyone she cared for and love to be put in danger and thus had allowed Yuna to find her and use Akiho to steal her powers and kill her and possibly destroy the world.
A shocked and guilt-ridden Akiho, feeling ultimately heart-broken and betrayed for being used, weeps and apologuises to Sakura for not realising this and wishes to never have moved to Japan, feeling responsible for her actions. The tears of the two then join together and breaks Kaito's hold, releasing Sakura from the dragon and the book and the spell that forced everyone to forget about her is removed.
Sakura finds herself in a castle-like room at the Temple where Akiho awakens, also free from the spell where the shocked Kaito and Mono see this. Despite Sakura having broken free, Kaito tells her that she has no power and thus he is the controller of the Clear Cards now as they obey him.
Sakura, still believing everything was her fault, pleads Kaito to stop and take her life instead and leave everyone alone, while saying that she hadn't meant to simply brush the Sakura Cards away and wants to restore them, saying that it was probably best if she never found them so that they would've been safe from her heart and her actions and no one would have gotten invovled with her crime.
Her tears and offering to sacrifice herself ultimately restores the power of her inner Star, and restores all of the Sakura Cards and her Star Wand, which also breaks the sleeping spell on Sayoran, Kero, Yue and Toya who, along with Tomoyo, rush to save Sakura.
Furious that her powers have been restored by accepting her actions, Kaito ignores Akiho's pleas to stop and fights Sakura with the Clear Cards, while Sakura fights back with the Sakura Cards in a duel of Card Magic.
Sakura attempts to stop Time with the Time Card and use the Return Card to convince her younger self to not look for the Clow Book, but Kaito uses the power of Time stop her from doing so, making her and Akiho realise that as long as he has the Watch, he is unstoppable.
Mono joins in the fight by transforming into her true form, but the timely arrival of Kero in his Cerberus form stops her and Sayoran shields Sakura, revealing that he had no choice but to use a spell to have all of the Sakura Cards to transfere into the Teddy Bears for save keeping until Sakura had figured out what happened, and apologises for not telling her.
Yue joins in the battle but Kaito over powers them, before beginning to absorb all of the Clear Cards and Sakura's Dream Key into the Watch, his intention to reverse Time to when he was expelled from the "D" Clan to destroy them and become the ultimate
Sorcerer of the world, with it's people under his rule and originally intended on using the Sakura Cards, but because of what Sayoran had done, he had no choice but to have Sakura create 'replacements' while using Akiho since she is much more powerful than Sakura will ever be.
Akiho, unwilling to allow Kaito to kill her friends and change history, attempts to draw the Cards and Key from Kaito who attempts to use the Watch to stop her from doing so, but Sakura, unwilling to let Akiho get hurt, uses the Hope Card as a last resort.
The Former Nothing Card gives out energy of Love and increases the strength of the hearts of Sakura, Sayoran and Akiho, allowing Sakura to knock the Watch from Kaito's hand and catches it, and allowing Akiho to steal the Dream Key and the
Clear Cards from Kaito who is now exhausted. He attempts to use his magic to kill everyone, but the sudden arrival of Eriol, his Guardians and the Magician D Clan create a barrier around him and disabling most of his magic due to over-using it.
The "D" Clan punish Kaito for his betrayal by removing all of his magical powers and send him into another dimension as punishment for his crimes, having Mono and Akiho's Book to be sealed away forever.
Eriol, having also gained a new Staff due to Clow Reed's having been severally damaged, tells Sakura the real truth behind Kaito's intentions, that Sakura inadvertedly allowed her magic to go out of control due to over-bearing excitement as she grew older and that her original Star Key acts as a barrier in her sleep to keep her powers from going out of control as long as she wears it.
The guilty Sakura, still regretful for her actions, asks if time should be reversed to prevent her from endangering everyone she cared for and loved despite knowing that she would never be with Sayoran, believing that their love is forbidden. The "D" Clan, however, with a change of heart, say that love is not forbidden in the world of magic after having sensed and seen
Sakura's will to sacrifice herself to save the world and those she loved, which restored the Sakura Cards and broke Kaito's spell. They do warn, however, that she should not use magic with proper guidance and tasks Kero and Yue to continue their task to teach her and guide her, which they promise they will and Sayoran vows to protect Sakura and train her to control her magic.
The Clan and Eriol also warn Sakura that she cannot keep both sets of Keys and Cards and has to make the ultimate choice to erase either one, even though the Dream Key and the Clear Cards will eventually lead her to die young, the same way Clow Reed had when he created the Clow Cards.
Unable to allow the Sakura Cards she'd converted to die, seeing them as her friends and loved ones, and not wishing to go down the same path as Clow Reed, Sakura hesitately chooses to erase the Dream Key and the Clear Cards. This act also strips Akiho from her magical powers and rendering her into a normal girl as she was also warned that her magical powers are too dangerous and had to choose to join the D Clan forever or become a normal human, which Akiho, not wanting to endanger Sakura or anyone else again, chose to lose her powers.
Due to Kaito's magic being taken and the Clear Cards erased, the Theme Park that was constructed over Clow Reed's house is also restored and everyone's memories of the events of "The Sealed Card" is finally restored, yet Akiho is left homeless.
With nowhere else to go and her family not wanting her, Sakura and her friends offer to have Akiho live with them. Akiho decides to live with Sakura and the D Clan, thanking Sakura for her actions, leave with a promise to Eriol that they will be careful with magic and make a fresh start of their own, while erasing the memories of Kaito from all except Akiho, Sakura, Sayoran, Kero, Tomoyo, Yue, Eriol, Ruby and Spindal.
Three months later, Akiho is adopted by the Kinomoto family and is now Sakura's and Toya's adoptive sister. The Sakura Cards and the Star Key remain alive and the same, under Kero and Sakura's watchful eye.
They both still attend Junior High School, with only them, Sayoran and Tomoyo having memories of Kaito's existance, and every second weekend during their dates, Sakura undergoes training with Sayoran to control her magic so that it won't go into haywire again, while Akiho gains her confidence in herself and continues to join Tomoyo in the Choir Club, while also having joined the Manga Club to one day become an Authoress of her own book series.
Toya still keeps secret of his sister's involvement, but gradually warms up to Sayoran, knowing that he can't keep Sakura forever, Kero returns to normal and still plays video games and Online games with Spindal.
Life has returned to normal, but Sakura vows to never dismiss the Sakura Cards or her Star Key ever again and to keep control of her inner magic from now on.