The Second Raid follows the events of the Full Metal Panic novel “End of Day by Day”, with some minor changes and additions made. The anime begins with Mithril disrupting military attacks in a Baltic nation. The leader of the Baltic military has somehow acquired advanced weaponry, most notably anti-ECS missile (missile able to detect systems with ECS invisibility). Due to these setbacks Sousuke must use the Arbalest to destroy the missile installations to allow the helicopters filled with refugees to escape. Since the end of the first series Sousuke has learned how to better control the Arbalest's Lambda Driver, but only slightly. In the following episode we are introduced to the main villain of the series, Gates. We later learn he is an operative of Amalgam, a mysterious organization that seems to be an opposite of Mithril. Causing terrorist acts, rather than preventing them. They are the organization that provided the Baltic army with these new weapons. We are also introduced to Xia Yu Fan and Xia Yu Lan, twin sisters who initially seem loyal to Gates.

Following this we are presented with a short school related side-story, and then Mithril begins it’s next mission in Nanjing. The purpose of the mission is to rescue hostages taken by Gates and are being held in a sewer-like facility. Due to communications problems transmitters will be used, which requires the help of one of Mithril’s scientists, Vincent Blueno. Before the operation Sousuke asks to use an M9 as opposed to the ARX-7 Arbalest. His proposal is denied as he is the only one able to pilot the Arbalest, this begins Sousuke’s hate for the Arbalest and it’s unreliable Lambda Driver. During the operation, Blueno leaks the radio transmissions to Gates who uses it to his advantage. During the mission, Kurz Weber struggles against Xia Yu Fan, piloting the only Zy-98 Shadow-type Arm Slave in the battle, while Melissa Mao and a team of Mithril's infantry deal with Xia Yu Lan, who posed as one of the hostages, and Sousuke is left to face Gates, who is operating a Venom-type Arm Slave. By using a quickly thought out plan after discovering they were being bugged, the De Danaan is able to use the radio information against Gates and lures him into a trap of their own. The terrorists are forced to flee when Gates's Arm Slave overheats, but the operation is still successful.

Following this, Vincent Blueno also escapes and is followed to Italy, where he is brought in by Mao and Kurz, with help from Sousuke. After being tortured, Blueno admits to being hired by Amalgam. It is here that Mithril first discovers the name, and even the existence, of the opposing organization.