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 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
- 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
- EM-CBX001 Hysterica
- EM-CBX002 Cleopatra
- EM-CBX003 Raziya
- EM-CBX004 Theodra
- EM-CBX005 Victoria
- EM-CBX006 Eirene