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!''The Battle of Aces''
The first game of the ''[[AlternativeContinuity Potable]]'' [[AlternativeContinuity Continuity]] is about the ''Dark Piece Incident'', where the nine heroes are involved and each character has his/her own story route. However, most of the story routes are contradictory with each other, leaving only a few of the events being {{Canon}}. Due to the small cast, the story is strongly focused on the Yagami family.

The ''Dark Piece Incident'' takes place directly after the ''Book of Darkness Incident''; the story begins that a [[PhantomZone force field]] appears around Uminari City and the remnants of the Automatic Defense Program/the Darkness of the Book of Darkness/[=NachtWal=] are revived, in form of the Dark Pieces, darker and negative versions of the nine heroes. The programs of the ''Eternal Ring''[[note]]revealed in the sequel[[/note]], the ''Materials'' (who are believed to be remnants of [=NachtWal=] in this game) are the ones who are summoning the Dark Pieces. The goal of the Materials is [[OmnicidalManiac bringing darkness and destruction over the world]] and a few mentions state that they want to revive [[BiggerBad U-D]], whose upcomming revival is the reason of the revival of the Materials in the first place.

In general, each character has to defeat the Dark Pieces in order to keep the city in save. Defeating the Materials will reduce the production of Dark Pieces drastically. Every character has also his/her own personal conflict, but its resolved after defeating a certain character. Whenever a hero(/ine) defeats the respective last enemy, the story skips the part where the rest of the Dark Pieces would be defeated, and the aftermath of the incident are shown, which usually takes place three months later. The story of the second game will take place at that time.
!''The Gears of Destiny''
The second game is about the ''Unbreakable Dark Incident'', that not only involves the revived Materials and new Dark Pieces, but also [[TimeTravel time travelling]] characters. Unlike the previous game, the sequel doesn't have story routes for each character, but a long story with twelve levels named as "Sequences", where all characters are involved. Each Sequence has its own main character(s) who have to fight the "targets" to continue the story. If there are multiple playable characters or targets, the player has the right to choose them, which can (but not always) affect story.

The first eleven Sequences are about the main story, the ''Unbreakable Dark Incident'', and the 12th Sequence is the PlayableEpilogue, which takes place a few months after the main story. The nine heroes from the previous game reappear again, as well as the three {{Secret Character}}s, the Materials. Eleven more characters, including [[BigBad U-D]] appear in the sequel. The two new main characters, Amitie Florian and Kyrie Florian, as well as the Materials, play a major part in the story.

The prologue is told by a young Amitie Florian, who introduces her family and herself. The Florian family are living on the different world Eltria. She tells her younger sister, [[WhenYouComingHomeDad Kyrie]], that Professor Granz Florian's work is important for humankind. To help their father's job, the sister have to grow up so they can support him.

!!Sequence 01
!!!Main character: Amitie Florian; Sub-character: Kyrie Florian
* '''Amitie's targets:''' Kyrie, Yuuno or Arf, Dearche
* '''Kyrie's targets:''' Hayate or Reinforce

Kyrie uses a TimeMachine to travel through time and dimensions and arrives at the ''A's Portable'' timeline. She is pursued by her older sister Amitie, who confronts her that time travelling causes a lot of problems in this timeline and that's their duty to protect time and destiny. The younger sister does not listen to her and they start a battle. It first looks like that Kyrie has lost, but it's just an act and Amitie feels the effect of the Virus Bullet that Kyrie used on her. The younger Florian takes the chance and escape.

The infected Amitie looks for help regarding the virus and she encounters Yuuno/Arf -- depending which character you choose, the dialogue between Amitie and them will vary if you choose them later in Sequence 02 and 03 -- however, because of Amitie's terrible communication skills, she accidently starts a battle. She's too exhausted and falls from the sky. Then Yuuno/Arf is contacted by Nanoha/Fate and then the duo is informed by Shamal that a high magical power force is rising and they are going to find it.

Meanwhile, Kyrie faces Hayate and Reinforce -- in promotional materials, she fights Hayate -- believing that Hayate is "Lord" Dearche, but she learns that Dearche is killed three months before. Suddenly, Dearche is revived and uses a bind spell on them. Before Dearche can finish them off, Amitie, who overcame the virus with fighting spirit and hot-bloodedness, arrives and save them. To everyone's surprise, Dearche loses against her and Hayate and Reinforce use the chance to kill her again, but Stern the Destructor and Levi the Slasher come to save her. It's revealed that the rebirth of these two Materials consumed a lot of Dearche's mana, which is the reason why she lost. Then, Kyrie makes a surprise attack, injures Amitie and Reinforce and she's siding with the Materials to help them to revive System U-D. The four of them escape and Amitie disappears as well. In form of three duos, Hayate and Reinforce, Nanoha and Yuuno, and Fate and Arf have the mission to find the Kyrie sisters and the Materials.

Playing this Sequence will unlock Amitie Florian.

!!Sequence 02
!!!Main characters: Nanoha Takamachi, Yuuno Scrya
* '''Nanoha's target:''' Amitie, Liese, Einhard Stern
* '''Yuuno's target:''' Amitie, Liese, Vivio, Stern

Nanoha and Yuuno can find Amitie and they offer her their help, but she refuses and escapes -- in promotional materials, she fights Nanoha. The two of them later meet Lieselotte and Liesearia, who mistakes them for Dark Pieces. Surprised by their strength, the twins are about to go full out, but Nanoha and Yuuno convince them that they are real. It's the revealed that the twins are ordered by Admiral Letty Lowran to delete the spreading Dark Pieces. When Nanoha and Yuuno continue their mission, the twins feel a dimensional quake.

Vivio and Einhard from the ''[[Manga/MagicalGirlLyricalNanohaViVid ViVid]]'' timeline are suddenly falling from the sky, but their Hybrid-Intelligent Devices, Sacred Heart and Asterion, provide them flight abilities to save them. Vivio recognize Uminari-City, her mother's hometown. The children enter in their Adult Modes when they feel magical powers in the near. Vivio meets Yuuno and Einhard meets Nanoha, realizing that they are in past and fly from Yuuno and Nanoha away.

In the end, Nanoha and Yuuno find Stern, who asks them politely for a mock battle -- in promotional materials, she fights Nanoha. Stern is in good terms with them, but she flies away to help her king reviving U-D.

Playing this Sequence will unlock Yuuno Scrya, if you play all battles with him chose him as a target in Sequence 01 before.

!!Sequence 03
!!!Main characters: Fate Testarossa, Arf
* '''Fate's target:''' Kyrie, Dark Piece Rynith, Dark Piece Presea, Levi
* '''Arf's target:''' Amitie, Dark Piece Rynith, Dark Piece Presea, Levi

Arf finds Amitie, but the result is the same as before. Fate finds Kyrie and offers her help, but Kyrie turns it down and mocks her instead. They fight against each other and Kyrie is surprised by Fate's speed, but she is able to trick Fate with the story about her father and disappears, though Fate has the feeling that Kyrie was saying the truth.

Both, Fate and Arf, face each a Dark Piece of Rynith and a Dark Piece of Presea. The choice, which character you play against Dark Piece Presea, will effect the story of the Sequence. If you choose Fate, she is sad that she defeated the copies of Rynith and Presea, but she will go onwards and then she she fights, in a good mood, against Levi. If you choose Arf instead, Fate is very depressed that she sliced her master and her own mother, resulting that Arf is so enraged that she blames everything on the Materials and fights Levi with all of her anger.

Regardless which character you choose, Fate befriends Levi, who gives them information about their goal. Dearche wants to revive System U-D to obtain infinite power and the Materials will find a place where they can live. Like Stern, Levi disappears to help her king.

Playing this Sequence will unlock Arf, if you play all battles with her chose her as a target in Sequence 01 before.

!!Sequence 04
!!!Main characters: Hayate Yagami, Reinforce Eins
* '''Targets:''' Thoma, Liese, Dearche, U-D

Like Vivio and Einhard, Thoma Avenir and Lily-Strosek from the ''[[Manga/MagicalRecordLyricalNanohaForce Force]]'' timeline find themselves in the ''A's Portable'' timeline. When they feel someone is coming to them, they react and meet Hayate and Reinforce. Surprise by Hayate's appearance, Lily concludes that they are in the past and they fly away.

Hayate/Reinforce meets the Liese twins, who either mistake Hayate for a Dark Piece because she's too nice or Liesearia is angry of Reinforce and they start a battle. The conflict between them is only half solved when the battle is over.

Then, Hayate and Reinforce find Dearche, who fights them before she revives U-D -- in the promotional materials, she fights Hayate. After the battle is over, Dearche and Kyrie revive U-D, also known as Unbreakable Dark, who turns out to be a young girl. U-D detects Hayate and Reinforce as enemies and attacks them -- the percentage of U-D varies depending who fights her; against Hayate it's 5%; against Reinforce it's 6%. When the battle is over, Dearche, Stern and Levi greet U-D, but she impales them with her magic because U-D detects ''everyone'' as her enemies, regardless if she feels that's not true. The Materials erase and U-D disappears, who is pursued by Kyrie.

Winning the battle against U-D with both, Hayate and Reinforce, is required for unlocking Sequence X.

!!Sequence 05
!!!Main characters: Signum, Vita, Shamal, Zafira; Sub-character: Kyrie
* '''Signum's targets:''' Dark Piece Thoma, Dark Piece Presea, Dark Piece Levi
* '''Vita's targets:''' Dark Piece Einhard, Liese, Arf
* '''Shamal's targets:''' Dark Piece Yuuno, Dark Piece Vivio, Kyrie
* '''Zafira's targets:''' Dark Piece Stern, Dark Piece Rynith, Dark Piece Dearche
* '''Kyrie's target:''' Combat Mode U-D

!!Sequence 06
!!!Main characters: Chrono Harlaown, Liese (Lieselotte and Liesearia)
* '''Chrono's targets:''' Levi, Nanoha or Vita, Liese
* '''Liese's targets:''' Kyrie, Fate or Signum, Hayate

!!Sequence 07-R
!!!Main character: Rynith
* '''Targets:''' Nanoha, Signum, Reinforce

!!Sequence 07-P
!!!Main character: Presea Testarossa; Sub-character: Rynith
* '''Presea's targets:''' Chrono, Dark Piece Fate, Zafira or Shamal, Rynith
* '''Rynith's target:''' Presea

!!Sequence 08
!!!Main characters: Vivio Takamachi, Einhard Stratos, Thoma Avenir
* '''Vivio's targets:''' Dark Piece Einhard, Thoma, Zafira, Nanoha
* '''Einhard's targets:''' Dark Piece Vivio, Thoma, Yuuno, Fate
* '''Thoma's targets:''' Dark Piece Thoma, Vivio, Hayate, Vita

!!Sequence 09
!!!Main character: Kyrie Florian
* '''Targets:''' Chrono, Shamal, Amitie

!!Sequence 10
!!!Main characters: Stern the Destructor, Levi the Slasher, "Lord" Dearche
* '''Stern's targets:''' Dark Piece Dearche, Dark Piece Vita, U-D
* '''Levi's targets:''' Dark Piece Stern, Dark Piece Zafira, U-D
* '''Dearche's targets:''' Dark Piece Levi, Dark Piece Signum

!!Final Sequence
!!!Main characters (first round): Signum, Vita, Einhard Stratos, Zafira, Shamal, Chrono Harlaown, Kyrie Florian
!!!Main characters (second round): Nanoha Takamachi, Fate Testarossa, Unison Hayate Yagami, Amitie Florian, "Lord" Dearche TRINITY, Vivio Takamachi, Thoma Avenir
* '''Target of the first round:''' U-D
* '''Target of the second round:''' Combat Mode U-D

!Sequence X
!!!Main character: Yuri Eberwein
* '''Targets:''' Stern, Levi, Kyrie, Dearche, Amitie