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, at Canicatti, 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.
For Sousuke to assist Mao and Kurz in their mission to capture Blueno, he leaves school yet again, adding to his string of absences. Kaname becomes worried about his grades, and Mao also worries over his future. Sousuke begins to reflect upon his life and begins to realizes he needs to start thinking ahead. It seems he decides he would like to remain a student. This is shown when Kyoko points out the fact that his hair has grown long and rather than cutting it himself he opts to go to a hair salon, like a normal high school student would. However, being his first time, his instincts again work against him and he ends up mistaking the haircut for another trap. This leads to Kaname offering to cut his hair for him and a touching scene is presented where Sousuke realizes how much Kaname is depending on him. The episode ends when Sousuke (who is beginning to realize his feelings for Kaname) is ordered to withdraw from guarding Kaname immediately, with all guard duties being entrusted to another agent, codenamed "Wraith."
After being called back, Sousuke falls into a slight depression, not wanting to pilot the Arbalest and wishing he were back at Jindai High. We are introduced to the new Uruz-1 (Urzu-1), Lieutenant Belfangan Groseaux. He tests Sousuke’s ability with the Arbalest, a test Sousuke fails miserably to the extent that Groseaux described Sousuke's moves as "Skilled but not artistic". Meanwhile Kaname is becoming increasingly suspicious that someone is following her. She discovers that Sousuke has left for good and realizes she is now completely alone. She decides to find out who is following her, and through a series of events discovers Wraith, who informs her that aside from himself, someone else seems to be following her. We discover this person is Xia Yu Lan, the younger twin. She shoots Wraith and then attacks Kaname. Kaname escapes, but is pursued and manages to surprise Yu Lan and shoot her with a Taser. After this she is met by Leonard Testarossa, Tessa’s brother and a fellow Whispered. He is an agent of Amalgam and has orders to suppress Yu Lang. She, however, refuses to comply, stating that she will continue her attempts to kill Kaname no matter what. She then tries to kill Leonard, but one of his bodyguards intercepts her. He then orders it (a miniature AS unit) to kill her. When this is done he expresses that he seems to have fallen in love with Kaname and steals her first kiss, which infuriates her. In exchange for her forgiveness, Leonard allows her to take back Wraith who seems to still be alive.
Back at Mithril the next mission is under way. It seems that someone piloting an AS unit is wreaking havoc in Hong Kong. The AS is equipped with a Lambda Driver and ECS and is piloted by Xia Yu Fan. Acting apart from Amalgam, she has done this at the wish of her Sensei, who we later learn also orders Yu Lan to kill Kaname. These two actions are what prompted Amalgam to kill the younger twin. Due to the ECS, the Chinese are unable to discover the location of the AS. Sousuke, Mao, Yan, and Wu are sent in to find the AS, while the rest of the Uruz (Urzu) team stand by to destroy it when it is found. During the mission Sousuke cannot concentrate due to recurring thoughts of Kaname. These distraction eventually cause him to crash the vehicle he is driving. Mao tells him she won’t work with him unless he can focus. Sousuke realizes he can’t and abandons the mission. Meanwhile tensions between North and South China force Mithril to order an assault on the enemy AS before it is found. While they battle the AS, Sousuke wanders through Hong Kong, eventually meeting a Chinese Woman who resembles Chidori. He goes with her to her apartment, most likely to have sex, but due to her appearance thoughts of Chidori constantly fill his mind. He decides to leave and eventually finds a newspaper that has a personal ad reading “To the son of Bdakshon’s Tiger. Meet Hamidra at Tsim Sha Tsui.” Essentially we learn that Sousuke was raised by a guerrilla fighter named Bdakshon’s Tiger, the rest leads Sousuke on a paper trail that brings him to the writer of the ad. This person turns out to be Gauron, who survived the self destruction of his AS at the end of the first series. We learn that he raised Yu Fan and Yu Lan long ago and they are carrying out his biding before he dies. He also tells Sousuke that Kaname is dead and pities him for becoming so weak. Sousuke ends up killing Gauron (for good this time), and feels as though he has no reason to live anymore.When the battle with Yu Fan seems like it cannot be won, Tessa orders the Arbalest to be sent to Sousuke to pilot. When it arrives Sousuke has no intention of piloting it, viewing the AS as a piece of scrap metal. As he turns to leave the scene he is confronted with Kaname, who used Wraith to find Sousuke. After beating him up she tells him he needs to pilot the Arbalest and save everyone. Feeling renewed confidence at seeing Kaname alive Sousuke finally realizes that he is the only one who can pilot the Arbalest and works together with the Al to fully make use of the Lambda Driver.
The final episode features the climax of the show with an AS battle between Sousuke and Gates. Gates, having been ordered to kill Yu Fan, decides to take out the Uruz (Urzu) team after his mission is complete. Sousuke arrives just in time and uses the Lambda Driver to its fullest potential.
The Second Raid ends with Sousuke finally understanding what he wants to do with his life: Pilot the Arbalest for Mithril and attend school with Kaname. He works out a deal with Mithril that allows him to do just that. We are left with both Kaname and Sousuke having realized their feelings for each other, but neither of them being able to admit it.