A joint training exercise between the Japanese Ground and Maritime Self-Defense Armies that takes place within the sealed sector of New Port City's Refugee District goes awry, putting the Asian refugees in danger. Section 9 Chief Aramaki takes the matter up with Kubota, his friend at the Ministry of Defense. While there, Aramaki is approached by a man from the Cabinet Intelligence Service: Kazunoto Gouda. Acting as a representative for his superior, the Chief Cabinet Secretary, Gōda requests that Aramaki bring the full force of Section 9 to bear on the situation. There's just one catch...

The episode was rated 8.03 from 106 votes.

Following a tip, the Major conducts an undercover investigation of Kuze in Taiwan. While there, she saves a boy running from the Mafia. After being saved, the boy follows her, making sure that she finishes what she started. The mafia will continue to pursue the boy and the Major has to protect him.

The episode was rated 8.03 from 86 votes.

A cat thief named Cash Eye has infiltrated a building owned by Federation of Economic Organizations Chairman Tsutomu Tadokoro. The cat burglar made quick work of the top-notch security system and left a calling card on the Chairman's desk saying that Cash Eye will be infiltrating his vault during an upcoming party. Albeit reluctant to get Section 9 involved, Aramaki has no choice but to assist Tadokoro. Prime Minister Kayabuki has requested that his unit go undercover in order to prevent the burglary.

The episode was rated 8.09 from 117 votes.

Armed terrorists have taken over the Chinese Embassy in New Port City. Holding an unknown number of hostages, the group, calling themselves the Individual Eleven, are demanding that the government cease accepting Asian refugees and dissolve the five Asian refugee camps situated throughout Japan. The members of Section 9 have mobilized and are in position to move in. However, due to the events of the Laughing Man Incident (1st GIG), Section 9 technically no longer exists. The unit must wait for an official order from Chief Aramaki, who is busy making his case in front of the new Prime Minister of Japan.

The episode was rated 8.10 from 134 votes.

The Major and Batou are flown to Berlin in an effort to track down a terrorist called "Angel's Feathers". While there, Batou attracts the attention of a young girl in a wheelchair. The girl is waiting for the yearly visit from her father, but Batou's appearance piqued her curiosity. As the days lead up to her father's visit, her curiosity in this stranger grows stronger.

The episode was rated 8.18 from 90 votes.

Much to the chagrin of Batou, Motoko, and the rest of the team, Kuze and the refugees manage to escape in one of the camouflaged boats. They are further hampered when an explosion causes heavy losses, leaving them unable to follow the fleeing boat. Regrouping, the team decides to refocus the investigation to the events surrounding Kuze. They start a secret investigation into Sagawa Electronics, the company responsible for the nuclear material transaction, and find that Gouda was involved. Meanwhile, as the boat heads for Dejima, Kuze makes his own unsettling discovery.

The episode was rated 8.19 from 85 votes.

Section 9 heads to Etorofu in search of Kuze. During their investigations, the Major finds an interesting floppy disk on the body of a dead addict. The floppy proves to be a goldmine of information, as it contains records of plutonium transactions. The last buyer to purchase the material was a group of Asian refugees. Realizing the transaction is about to take place, the team rushes to the location and is surprised by what they find.

The episode was rated 8.21 from 81 votes.

Several bombings have occurred throughout New Port City. Each time, Section 9 arrives too late to stop their detonations. With a fifth and final bomb set to go off somewhere in the city, the unit puts all of the information they have found from the first four bombings together. Even the Cabinet Intelligence Service is having their fair share of difficulties. A hacker has infiltrated its incredibly advanced computer security system. The hacker enters the vast array of information stored at the CIS and begins to collect data...

The episode was rated 8.21 from 80 votes.

The Chief Cabinet Secretary uses the excuse of the refugees possessing 10kg of plutonium to mobilize the military against Dejima. With the available evidence against the refugees, Prime Minister Kayabuki reluctantly agrees. However, she soon learns from the Chief Cabinet Secretary that he's aligned himself with Imperial America and is now after her job. Knowing her days as P.M. are numbered, she agrees with Aramaki's plan and calls the U.N. in for a nuclear inspection of Dejima. The move buys them some time to defuse the situation, and Section 9 heads to Dejima to meet up with the U.N in two days. However, with tensions running high it is only a matter of time before someone fires the first shot.

The episode was rated 8.29 from 85 votes.

Section 9 has uncovered Shō Kawashima's ("FAKE FOOD") external memory device on the net. Hidden in a route to the Asian matrix only accessible through the European array, Section 9 concludes that the device was hidden by Gouda. Unfortunately, Gouda has left no trace of his movements in the device. The Major prepares to dive into the device with Bōma and Ishikawa watching her closely. However, before she can dive, Aramaki notifies her that someone even more important than the external memory device has just surfaced...

The episode was rated 8.31 from 89 votes.

With the felling of Dejima Bridge by the refugees, a rumor circulates around the Cabinet that the refugees plan a mass suicide bombing using nuclear bombs. Fearing this, the Cabinet steps up the attack against the city. Meanwhile, Prime Minister Kayabuki has been secretly arrested and taken to an unknown location. Aramaki, Togusa and Proto, in trying to help the P.M. are also taken into custody and secured in her office. With Section 9 having entered the non-communication zone and Aramaki being cut off from communication, Ishikawa and a Tachikoma make their way to Spring-8 on their own. Meanwhile, Gouda has sent an unwitting Section 4 after Section 9 to retrieve the plutonium.

The episode was rated 8.48 from 88 votes.

While on an assignment guarding the Prime Minister, Saitou and the Tachikomas pass the time playing poker with a few policemen who are also assigned to the case. Much to the chagrin of the other men, Saitou wins hand after hand. The Tachikomas take notice of Saitou's uncanny accuracy and start to comment. Their constant chattering quickly gets on the other player's nerves, so to smooth things over Saitou recounts his time working as a sniper for mercenaries in Mexico.

The episode was rated 8.56 from 88 votes.

As the attack on Dejima escalates, the Major catches up with Kuze. She explains the whole situation to him and he agrees to follow her. They are about to leave when both are attacked by the Self-Defense forces and in the confusion are trapped under the rubble. Togusa rescues the Prime Minister and brings her back to her office. There, Aramaki hopes her influence will stop the launching of the ultimate weapon. Meanwhile, Batou reasons with Section 4.

The episode was rated 8.57 from 83 votes.

Training has commenced to find new recruits for Section 9. With Motoko acting as the target, Batou and Togusa watch as the recruits try to keep up with the Major. After ditching some of the recruits, Motoko has to lose just one more pair. She ascends some stairs in an alley and the recruits follow her. Moving out into the street above, the recruits see that they have lost the target. However, Batou and Togusa have lost contact with the Major as well.

The episode was rated 8.65 from 92 votes.

Kuze and the Major come up with a plan to save the refugees, but the chances of its success are slim. Realizing this, the Tachikomas disobey the Major's orders and come up with a plan of their own. Batou has also disobeyed the Major's orders to go to the bridge and is desperately searching for her in the ruins of Dejima. Meanwhile, the Prime Minister is frustrated with being spurned by the Chief Cabinet Secretary. Determined to be remembered as more than a mere figurehead, she takes matters into her own hands.

The episode was rated 8.79 from 94 votes.