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.

Following the Section 9 reunion, Kusanagi and her colleagues learn about the "post-humans," a previously unknown threat to humanity.

The episode was rated 8.21 from 24 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 Laughing Man returns to kidnap Ernest Serano, the CEO of Serano Genomics, just as he did six years before. Returning to the café where Serano was first kidnapped, he and the Laughing Man share the story of the events leading up to the kidnapping and the events following it. During the conversation, the Laughing Man asks Serano why he never fulfilled his promise to tell the truth about the Murai Vaccine, and in response Serano informs the Laughing Man that the whole time, he was under house arrest. Meanwhile, Section 9 determines the Secretary General Yakushima to be the man behind the Laughing Man scandal, and resolve to take Serano into protective custody to obtain his testimony. When the team discovers that Serano has been kidnapped by the Laughing Man again, they mount a frantic search to find and secure him.

The episode was rated 8.22 from 123 votes.

The dismantling of Section 9, spun by the media as a JSDF preemptive strike against a radical security unit planning a coup, provides the Prime Minister with the public support his party needs to win the Lower House elections. Immediately after the election, in keeping with his promise, the Prime Minister discloses the information regarding The Laughing Man case, fingering Yakushima as the ringleader. Three months pass, during which Togusa tries to come to terms with all that has happened with Section 9. In his attempts to find information on the rest of the team, he learns that the Major was killed and the remaining members of Section 9 are serving time in a state prison for high treason. The news upsets Togusa, and he resolves to assassinate the man responsible for Section 9's dissolution.

The episode was rated 8.29 from 127 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.

Togusa finds himself in the hospital after being shot, but is desperate to impart what he has learned to the rest of the group. By diving into Togusa’s memories, Section 9 experiences the DEA raid against the Sunflower Society firsthand, prompting anger and rage. The Chief takes it upon himself to notify the head of the DEA of Togusa’s presence at the Sunflower Society building during the raid, prompting the DEA chief to order the Narcotics Suppression Squad (NSS) to the house of Dr. Hisashi Imakurusu. Dr. Imakurusu had overseen the board that denied the Murai Vaccine; after being diagnosed with Cyberbrain Sclerosis, he began using the vaccine in secret and subsequently went into hiding. Section 9 believes Dr. Imakurusu may hold a clue to unraveling the entire Laughing Man case, and undertake a desperate search to locate him.

The episode was rated 8.38 from 138 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.

Aramaki has been released under his own recognizance, and meets with the head of the Ministry of Justice to explain the situation and ask for help in ensuring his team's safety, but the Minister of Justice is powerless to affect the situation beyond the prosecution of Yakushima. Elsewhere, Saito and Ishikawa are caught in separate traps set by Umibozu teams, but not before successfully dispersing information seeds given to them by the Major. With Batou and Kusanagi as the only uncaptured members of Section 9, Batou undertakes a risky sortie to the Major's apartment to recover her sentimentally-valued watch. Before he can escape, Umibozu commandos arrive and a firefight ensues. Batou successfully fends off the first wave of attacks, but is unexpectedly confronted with two armoured combat suits, the second of which proves to be more than he can handle.

The episode was rated 8.53 from 125 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.