外交大臣及其秘書、後援會長、兩名北美產業振興會客人被藝妓機器人拘為人質，久保回代表軍方表示要介入，與不願放權的警方發生爭執，最後此事交由9課處理。突擊救出人質後定位了病毒釋放者，博馬、巴特等人抓住嫌犯，但後者燒燬電子腦中的記憶。久保回告訴荒卷外交大臣的秘書是情報人員，正在調查大臣突然對 「一之瀨報告書」感興趣一事，這是一份在非常時期生效的外交軍事計劃，認為她的死有隱情，9課介入調查。陀古薩發現大臣被換腦，對方利用大臣的軀體接觸到了那份報告書並準備逃往美國，在機場被及時攔截，大臣的電子腦也被取回。

巴特給自己的塔奇克馬使用天然機油。播磨研究學園劍菱重工一台新型戰車在調試中失控，九課出動阻止。經調查得知同事根據戰車設計者之一加護武的遺願在他死後將大腦接入戰車，取代原先的AI，加護武由於天生體質差對父母有怨恨，由於宗教的原因他無法進行義體化，他認為死後精神擺脫了宗教的束縛便作出這一舉動，九課認為他是想向父母報仇。同時荒卷與劍菱高層進行交涉以獲得戰車的數據並得到應對方法，劍菱方面出於商業利益不願透露，荒卷指出若此戰車造成重大破壞，軍隊是不會採購它的，最終劍菱妥協，九課用他們提供的專用黏膠阻止了戰車前進，素子正要取出加護武的大腦時，加護武的父母突然出現，為防萬一素子燒燬了他的大腦，但在向它注入病毒的瞬間，素子感到加護武的大腦處在複雜的情緒下，只是這已無法再獲悉了。

素子為了尋找笑面男的相關情報，而參加了一個名為笑面男聊天室的網絡聊天室。討論中，參與討論的成員「貝比魯斯」，在暗殺警視總監行動的當時，正在侵入現場的網絡，之後並在網絡上找到由七尾親手竄改並以七尾為名的認證服務器，從中發現到殘留了好幾個模擬過的計劃，例如再度恐嚇大型微機械企業、或鎖定改造人食品企業之類的計劃，但所有計劃都有一個共通點，計劃的成功關鍵都在於遲效性分割型病毒，但暗殺警視總監，卻不在原先的計劃中，貝比魯斯更大膽推測，這全是警方自導自演，但當時出現在暗殺現場的攻性防壁卻與警方布設的不同，未曾見過，推測這個攻性防壁是笑面男布下的。之後素子從貝比魯斯的手中得到暗殺總監當時攻擊素子替身防壁的攻性防壁。

16年前被極端團體興國旅團綁架的戶久良電子公司社長之女重新出現，海上保安廳在距沖繩島200海里的一個廢棄的海上工廠中發現了她與一群興國旅團成員在一起，相貌非常接近當年，DNA結果也符合本人。但不久先遣偵查的SST成員與基地失去聯繫。九課奉命調查。素子、陀古薩，巴特、齊籐分成兩組潛入，九課的支援飛機也在不遠處盤旋。平台甲板上竟十分熱鬧，因為附近的船員將它當作貿易集散地，巴特、齊籐循GPS信號找到了一名倖存者，但他精神受到了很大刺激，巴特認為這也許與他曾與對像女孩有過電子腦連接有關，倖存者說女孩成了領袖。另一面，素子、陀古薩找到了女孩，她正在與一名老太爭吵，素子接入女孩的電子腦，卻發現她並非戶久良小姐。此時興國旅團發現了入侵者開始反攻，激烈戰鬥隨即打響，九課增援趕來順利完成突圍。在飛機上人們發現那個女孩是戶久良小姐的女兒，而26歲的小姐卻因為長年的殘酷經歷急速衰老，那名SST成員就是讀取了對象電子腦後因為無法忍受而精神失常。

笑面男事件因德古沙的努力更進一步釐清，但德古沙因此受重傷。向日葵會大力讚揚村井疫苖對於電腦硬化症有非常良好的療效，但為何那麼好的藥卻鮮為人知～？

巴特為了想幫素子（少佐）取回她的手錶，而到了她的住處附近。另一方面，荒卷找法務部官員以求保住九課成員生還，但因藥島勢力過於強大，該官員也無可奈何。塔奇克馬（巴特專用機）在老人院頂樓工作告一段落後望著遠處的九課建築，爺爺交給它一顆炮彈，讓它堅定救人的心意。塔奇克馬回到原是九課建築的廢墟之中，看到巴特留下來的天然機油，此時另外兩架塔奇克馬（一輛被漆成黃色，另一輛是灰色的）也到了，三台塔奇克馬決定合作去救巴特…

素子少佐的意識在肉體被破壞前就已進入網絡，經過一段日子審問的德古沙被釋放，渾渾噩噩的過日子。他不想相信九課是被荒卷課長所背叛，可是在九課成員都被抓，甚至少佐被宣告死亡的情況之下，課長居然完全無任何音訊。原本德古沙想再找另一份普通的上班工作，但發現自己無論如何都嚥不下這口氣。他拿起自己的左輪手槍，走到藥島議員所在的建築前，卻有人搶先一步用槍抵著他的背…

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.

A botched arms deal reveals that the government's plans to remove Plutonium from the Shinjuku dig site ("EXCAVATION") by sea have been compromised. Section 9 is called in to take the Plutonium out of Old Tōkyō by land.

The members of Section 9 are not happy being used by the government. Batou is especially incensed since Section 9 is supposed to be an offensive organization. His patience will be further tried when he and Section 9 find out who will be accompanying them on their mission...

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.

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.

During a scheduled maintenance, the Tachikomas begin to chat away about the Individual Eleven.

While talking in their new "forum", Batou and Togusa appear and take one of the Tachikomas - who just happens to be Batou's pet - with them to Spring-8 to look at the scientific evidence gathered on the Individual Eleven.

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.

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.