Scenario 13: The Forbidden Sea
The plot begins similar to the end of the episode Fallen Princess.
On the Ptolemaios 2 Custom, Meleina interrupts a conversation between Sumeragi and Ruri to inform them that Princess Angelise from the Misurigi Empire was actually a Norma. A reporter elaborates on the events on the bloody crime scene outside the Dawn Pillar. In the Ptolemaios 2 hangar, the player learns from the characters that Norma are those discriminated for lacking the ability to use Mana, a power that can only be used by people from the Founding Nations, an alliance of that Earth's oldest, longest lasting nations. Among the Founding Nations is the Empire of Misurugi. Even with the Earth Federation around, the Founding Nations have a lot of influence giving orders even to the Atlantic Federation. The characters discuss the lack of compassion of the Founding Nations but note that it generates bad PR, prevent people from travelling to or from the Founding Nations.
The Ptolemaios 2 Custom and Nadesico B head to Area D of the Pacific Ocean where Arzenal is.
Scenario 14: Blood-Splattered Wings
Scenario 15: Island Encounter
In the Arzenal Hangar, Ange enquires Rosalie and Chris as to why her uniform was chewed up. Rosalie jokes that it was mice, prompting Ange to pull out a knife but she is stopped by Salia. Vivian says Ange is a little on edge, Ange blames it on the "gnats", insulting the Norma. Vivian shows Ange her Likitee key chain.
Scenario 16: Bonds Renewed
Scenario 17: Swooping Wings
Scenario 21: The Martian Polar Cap Ruins!
During the assault on the Martian polar cap ruins, a group of DRAGONs suddenly appeared out of a singular point, the first instance of DRAGONs appearing outside of Arzenal's vicinity. At the end of the battle, the team is caught in the battle between a large group of DRAGONs led by a mysterious Para-Mail and six black Villkisses led by a mysterious figure. In order to protect Akito, Yurika transports the entire team to another world using the Calculation Unit.
Secret Scenario: Thought Patterns
This scenario is unlocked if Sosuke Sagara obtains 40 kills, and the Full Metal Panic cast obtains a total of 100 kills. In order for Vilkiss to activate its Ariel Mode, Ange has to train under Sosuke. At some point, Ange gets tired and sneaks off in the Likitee mascot outfit, which is found in the hangar of the Yamato for some reason.
Sosuke caught on and dressed up as Bonta Kun. Bonta Kun thought that Likitee was attacking Kaname Chidori and fired at Likitee. When the Amalgam forces attacked Jindai High School, Vilkiss showed up to protect Likitee, knowing that Ange was in the costume. As payback for that earlier incident, Ange briefly fired at Bonta Kun.
If Bonta Kun were to fight a member of Amalgam, they get confused on why they're fighting a mascot. Guess they didn't expect to fight a cartoonish mascot on the battlefield today. They even proclaim that they're jokes if they got shot down by Bonta Kun.
When backup arrives for the duo, most of the girls want to keep Bonta Kun all to themselves. Even Salia couldn't resist Bonta Kun's cuteness. However, Salia manages to restrain herself and tells herself that she wouldn't be better than Rosalie if she were to focus on her obsession.
If Ange were to fight Gates, Gates comments on her attractiveness. Ange turns down Gates and tells him his sideburns are goofy. Gates somehow gets the idea that his sideburns are great. Ange is confused on how Gates managed to misinterpret her statement. Gates replies, "Because I'm the Great Gates, my lady!" This reply frustrates Ange to the point where she decides to shoot Gates down because she wants him to shut up.
After the scenario, Nine fixes up Bonta Kun, letting Sosuke wear it if the player desires. Vivian found the damaged Likitee costume and wondered who would do that, especially since it was a gift for Ange. Meanwhile, Salia has a secret tea party with Bonta Kun in her Pretty Salian outfit. It seems that she's a fan of the mouse-bear.
Scenario 30: Hometown of Betrayal
This scenario is an retelling of the episode of the same name.
Learning that her sister Sylvia is facing execution, Ange and Momoka decide to return to the Empire of Misurugi and rescue her. Unexpectedly, they receive help from Hilda, who also wants to escape Arzenal in order to see her mother.
Ange and Momoka jump to Misurugi using the Ariel Mode of Villkiss. Before they could sneak into the palace, however, Ange runs into her former classmate and friend, Akiho, who is terrified at the sight of Ange. Ange tries to calm her down, saying that she is still her friend, and Akiho appears to agree, but secretly tries to contact the police using Mana. Ange sees through this and ties her up.
Inside the palace, Ange kills several guards and the two reach Sylvia. However, Sylvia stabs Ange, calling her a monster. Ange's brother Julio appears and explains that Sylvia was never going to be executed, and the two put on an act in order to lure out Ange and kill her.
At Ange's public execution, Sylvia whips Ange while the watching crowd, including Akiho, cheers on. Julio thanks Momoka for giving him this opportunity, revealing that he was the one who arranged for her to reach Arzenal. Purple incites the crowd and encourages their rowdy behavior. Ange calls the crowd monsters, and Julio tells her to be silent. Ange tunes them all out with the Eternal Story song, and Tusk busts in to free Ange and Momoka. They escape, and Julio sends in unmanned drones to finish them off.
Like in the Secret Scenario, Vilkiss shows up to rescue Ange. Momoka even asks how Vilkiss did that feat since it had no pilot. The Nadesico C does a Boson Jump, and Ruri Hoshino claims that Ange is now under her custody. Julio asks why they Jumped in the first place, so Ruri claims that the Nadesico forces are autonomous. Julio invites the Nadesico forces to play war games with the drones. Unfortunately, the drones are using live ammunition, so the Nadesico forces use live ammunition in retaliation. Yurika even notes that "Emperor Brat" has pissed Ruri off.
Tusk and the others deploy from the Nadesico. The Mail-Riders talk about Tusk using a Para-Mail and wonder if he wears a suit like they do. Tusk tells them that's not the case. Ange asks if the others have seen Hilda, but they haven't found her. Ruri tells the group they have five minutes to escape and tell them to show these drones no mercy. If Tusk fights, he'll thank his parents and proclaim that he's Ange's knight. If Ange fights, she becomes determined to fight for a place where she can belong.
The Nadesico gets a warning from the Ptolemaios 2 about the arrival of Dragons at the Misurugi Empite. The group is shocked at their sudden appearance, and Julio asks the group to kill the Dragons. The Dragons must be stopped while the Nadesico retreats. Akito shows up with Hilda in another Boson Jump, and the Para-Mail Riders call Hilda a deserter. Athrun tells them to cut it out, which works since Chris and Rosalie have crushes on Athrun.
When Ange destroys an enemy with Tusk's assistance, the group finds about that incident on that island and talk about it until Ange tells them to shut up. If Hilda fights, she thinks her mother has forsaken her and curses the world for placing her in this situation. If Salia, Chris or Ersha fight, they sense a presence watching over them, hinting at their defection into the Diamond Rose Knights. If Vivian fights, she hints at the reveal of being a Dragon by noting that she doesn't feel like herself and asking, "What will become of me?" If Maito fights, Purple notes his presence. Maito senses the presence of an extremely frightening evil in the area.
When the Nadesico destroys the drones, Julio has a big breakdown. Ryoko says that Julio is a coward, and Ange agrees with her. Basically, Ange has disowned Julio and Sylvia after that botched execution.
In the Arzenal prison cell, Hilda talks about her problems with the others. A Dragon shows up and Shinn threatens to shoot it. It sings a song with Ange and turns back into Vivian. As a result, Ange demands some answers from Jill and Jill complies.
Universal Century Earth
Approximately three thousand years ago, this world was invaded by a race of mechanical aliens with god-like powers known as the Mycenaeans, who intended to take over Earth and use it as a forward base in their intergalactic conflicts. Embryo, one of the world's top scientific minds and theoretical physicists, used his invention, the Ragna-mails, against the Mycenaeans. Originally designed for interdimensional exploration, the Ragna-mails are equipped with powerful weapons known as Space-Time Convergence Cannons. While the use of these weapons led to the defeat of the Mycenaean Gods and their subsequent sealing within dimensional rifts, it also caused Dragunium - the primary energy source of this world- to detonate on a global scale, polluting the world and killing the vast majority of its population.
The survivors of the conflict used genetic engineering techniques to adapt to the now devastated Earth, becoming the Dragons. They sealed themselves within a barrier, and began the process of rebuilding civilization. Meanwhile, a different breed of civilization began developing outside the barrier, which would eventually become the Earth Federation over two thousand years later.
Despite being entirely separate from the outside world, a select few individuals in this world know of the Dragons' existence. One of them is Dr. Saotome, a scientist renowned for his research on Getter Rays, a powerful form of cosmic radiation, since Dragunium is actually the crystallized form of Getter Rays. He even named the second generation of Getter Robo after the Dragons, due to their natural ability to absorb Getter Radiation. Others who are aware of the Dragons include Dr. Hell and the commanders of Nerv, who all refer to them as "Hermits of Wings".
In order to create a brand new utopia, free from war and pollution, Embryo stole Aura, the first Dragon, from this world, and shifted to a parallel Earth, using the Dragunium energy of Aura to create the World of Mana.
Anno Domini Earth
Approximately five hundred years ago, Embryo shifted to this world, and created the Founding Nations. The residents of the Founding Nations are capable of using Mana, an advanced information sharing system capable of manifesting one's will into physical forms powered by the Dragunium energy of Aura. Through the use of Mana, the Founding Nations soon became free of war, poverty, and discrimination. However, humans who cannot use Mana due to the reemergence of ancient genes soon surfaced. Despite Embryo's best efforts, he could not prevent these "Normas" from being born. Therefore, he used them, spreading the idea that all Normas are dangerous and anti-social monsters and unifying the world of Mana against them.
When discovered, Normas are forcefully separated from the general population and sent to Arzenal, an island detention facility in the middle of the Pacific Ocean, where they are forced to combat the Dragons from the Universal Century world (who are attempting to retrieve Aura) in machines known as Para-mails. While officially, Arzenal's purpose is to protect the rest of the world from the Dragons, its actual purpose is the collection of Dragunium from the corpses of the Dragons, which is then used to fuel Aura.
The sea area surrounding Arzenal is known as "Area D", and is avoided by all air traffic and satellite orbits due to the electromagnetic disturbances generated by the Dragons' Singularities. The area is also patrolled by unmanned mobile weapons of the Founding Nations (including GN-X mobile suits and Euclid mobile armors), which indiscriminately attack anyone attempting to enter the area, and are responsible for recovering the corpses of Dragons, but do not assist the Normas in combat. The existence of Arzenal is kept secret, but the Orb Union, which is geographically close to the island, secretly supports the Arzenal personnel, and the Celestial Being is also aware of the existence of Arzenal and the Dragons (though not even Veda has access to in-depth information regarding Arzenal).
Since the Founding Nations hold great sway even among the Earth Federation, the other member states do not interfere in their affairs despite their inhumane treatment of Normas. However, because of this, travels to and from the Founding Nations are rare due to their poor public relations.
The original inhabitants of the world, the Ancient Humans, opposed Embryo's plans and rebelled against him many times. In order to combat Mana, they created technologies that can modify human genes. To obtain the power to defeat Embryo, one of them created an organization intended to rebuild the world through destruction. In response, Embryo created Blue Cosmos and Logos, and manipulated the Innovators into turning on the Celestial Being. In the end, the Ancient Humans were almost entirely wiped out. However, they managed to steal one of Embryo's Ragna-mails, the only weapon capable of killing Embryo, through many sacrifice, setting into motion the events of Cross Ange.
- Angelise Ikaruga Misurugi
- Salia Tereshkova
- Zola Axberg
- Hildegard Schlievogt
- Coco Reeve
- Miranda Campbell
- Tanya Zabirova
- Irma Kankkunen
- Emma Bronson
- Zhao Mei
- Sophia Ikaruga Misurugi (mentioned only)
- Jurai Asuka Misurugi (mentioned only)
- Julio Asuka Misurugi
- Sylvia Ikaruga Misurugi
- Momoka Oginome
- Unknown-class (called "Bighorn-class" in-game)
- Riza Randog
- Dr. Gecko
- Aura Midgardia (only known as "High Priestess" in-game)
- AW-CBX007 (AG) Villkiss
- AW-CBR115 Glaive
- AW-ZZR520 (ES) Hauser Ersha Custom
- AW-ZZR520 (CR) Hauser Chris Custom
- AW-GSX232 (VV) Razor
- AW-FZR304 (SA) Arquebus Salia Custom
- AW-FZR304 (ZR) Arquebus Zola Custom (cutscene only)
- AW-FZR304 (VN) Arquebus Vanessa Custom
- AW-FZR304 (HL) Arquebus Hilda Custom
- EM-CBX001 Hysterica
- EM-CBX002 Cleopatra
- EM-CBX002 Cleopatra Ariel Mode (appears in attack animation)
- EM-CBX003 Raziya
- EM-CBX004 Theodra
- EM-CBX004 Theodra Michael Mode (appears in attack animation)
- EM-CBX005 Victoria
- EM-CBX006 Eirene
- After Ange returns from Tusk's island, she remarks that Setsuna has a nice voice, referencing how both Setsuna and Tusk were voiced by Mamoru Miyano.
- During the battle with the Bighorn Dragon, Salia briefly confuses the Strike Freedom Gundam with the Villkiss, referencing the two's similar design. Athrun also comments on this and notes that the Villkiss' fighting style reminds him of "that guy".
- It is later revealed that the Freedom Gundam was based on the Villkiss, explaining the similarities between its successor and the Villkiss.
- The Aurora is absent from the game, most likely due to the large number of battleship units already in the game.