3rd Division vs. The Hollows is the event in which Amagai tries to promote the connection between the different Divisions in the Gotei 13, as well as Captain-Commander Genryūsai Shigekuni Yamamoto's Menos ruse to see how well the Gotei 13 handle themselves in an emergency situation. This event takes place in the Kasumiōji Conspiracy.
The 3rd Division members gather at the assembly hall, where they are greeted shortly after by Lieutenant Izuru Kira and 3rd Seat Makoto Kibune. As they apologize for their lateness, the Division wonders where their new captain is. Amagai is at a captains meeting proposing the idea of inter-squad cooperation, using the incident in the Dangai as a prime example of the Gotei 13's lack of communication between the divisions. 
Amagai states joint training is necessary to promote this concept, with Captain Kenpachi Zaraki dismissing it as a waste of time. Captain Jūshirō Ukitake, disagreeing with him, states the captains who defected from the Gotei 13 used this lack of contact between divisions to go about with their secret plans, and this idea could prevent further cases. Later, at the bar, Amagai is intoxicated, depressed by the viewpoint of the other captains. Captain Shunsui Kyōraku consoles him, whispering to Ukitake he got drunk off of the smell of the sake.
Ukitake reinforces Amagai's proposal, stating it will take a while for the Gotei 13 to agree as a whole. Amagai, overcome with happiness, hugs him in delight, much to Kyōraku's surprise. Amagai gets up and apologizes, finally feeling motivated, as he drinks the sake and collapses. Elsewhere, Captain Tōshirō Hitsugaya tells Lieutenants Renji Abarai and Rangiku Matsumoto about Amagai's proposition of joint training, which prompts Rangiku to imagine a possible scenario. She tries to persuade Renji to approve of it as Hitsugaya walks away.
Hitsugaya, knowing of Kyōraku and Ukitake's wholehearted support of Amagai's concept, hopes this does not cause dissension between the captains. Later, Izuru reports to the 3rd Division the proposal has been rejected, much to the dismay of the other members, who believe they will continue doing tedious tasks. As they comment on the ridiculous nature of tasks they were assigned, 3rd Seat Makoto Kibune walks in, stating two captains are supporting Amagai's idea, and tells them their opinions may soon change. Izuru stares off with Kibune, citing their previous conflict and his appearance at the Kasumiōji compound. When Kibune inquires what is wrong, Kira asks him why he entered the Kasumiōji compound the other day, and Kibune states he must have him mistaken for someone else. As Kira wonders whether it actually was him, his train of thought is interrupted by a Jigokuchō, which announces Menos have infiltrated Soul Society. Kibune states they should go out first, regardless of their captain's whereabouts.
As Kira refuses, telling them they should wait for their captain, Kibune, interrupting, states their training was more than sufficient to allow the Division to handle itself without the presence of the Captain. Kibune asks if he is prepared to disregard the Division's wishes in order to receive orders from Amagai, as it would ruin their morale. Kira, countering, states they do not have enough information to rush in blindly. However, the other members back Kibune up, stating they can more than handle it. As Kira refuses to take the lead, Kibune is forced to take up the mantle, and watches in shock as they wholeheartedly agree with Kibune's perspective. Meanwhile, the 11th Division, assembling, are searching throughout Seireitei for the Menos. Ikkaku Madarame states the 11th Division will get there first, but they are cut off by the 7th Division members, led by Lieutenant Tetsuzaemon Iba. As Ikkaku and Iba immediately start arguing, both divisions start squabbling over getting there first.
The 10th Division is searching for the Menos, but have not come across any sightings. Hitsugaya, leaving Rangiku in charge of the search squad, promptly leaves. Soon after, Rangiku comes across an area cordoned off by the 12th Division. When Rangiku asks about the sign, Mayuri, appearing, explains the 12th Division will capture them, as it is unheard of for Menos to appear in Soul Society. As Hitsugaya searches by himself, the Jigokuchō, issuing an update, states the Menos have now been narrowed down to the northeastern section of Seireitei. Upon hearing this, Iba and Ikkaku simultaneously issue orders for their search squads to head in that direction. Kibune and the other members of the 3rd Division search squad, puzzled by the recent announcement, state the Menos should be close by, but there are none. Kira approaches the group, particularly Kibune, and tells them to pull back, restating his previous reasons. The members berate him for saying that when they have already come this far, with Kibune, stating he was the one who was originally against the idea to leave, asking why he is even here.
A messenger reports to Kyōraku the search for the Menos has led them to find only the members of other divisions. Kyōraku, thanking him, asks Lieutenant Nanao Ise what she thinks of this. She comments on its strange nature, comparing it to being frustrated over an invisible enemy. Agreeing, he wonders if there are actually Menos invading. Hitsugaya, appearing, wonders the same thing. Kiyone and Sentarō are shocked that the Menos are a ruse, as explained by their captain.
Ukitake states all they have been hearing are announcements, but there has not been a single reported sighting. Realizing the whole incident was set up to show how easy it is for the Gotei 13 to fall into a state of confusion, he wonders who is responsible for this incident just as Yamamoto reveals himself as the instigator, much to his surprise. Kira faces off against Kibune, who, trying to tell him to stand down, resorts to the use of his Zanpakutō. Amagai, intervening, tells them to stop fighting and, apologizing for his lateness, tells Kibune not to overstep his authority as 3rd Seat.
As Kira feels an unusual Reiatsu appear, he notices a huge Menos towering over them. Amagai, asking what is wrong, turns to see five Menos have simultaneously appeared over Seireitei. All the search squads are seen converging to the 3rd Division's location, all competing to get there first. As the search squads converge together, they find themselves in a writhing mass of each other, unable to move. Yamamoto reveals his aim was to see how the 13 Divisions would react in light of false information, and wonders what Amagai will do during this situation.
Amagai, employing their training session layout, tells the other Divisions about their maneuvers as he releases his Bakkōtō, sending a bright green column into the air and notifying the other divisions of what they are about to do. He instructs the members of the 3rd Division to move the other search squads according to his instructions. With the use of the joint-attack principle, four of the five Menos are killed. Kira, smiling at his captain, notices Kibune reading information under his glasses.
After the last Menos is killed, Lieutenant Chōjirō Sasakibe reports to Yamamoto the success of the 3rd Division's methods in organizing the other divisions to combat. Yamamoto announces his approval of the joint-training sessions. At the 3rd Division barracks, the members are seen congratulating each other on finally stepping out of the shadow of Gin Ichimaru's betrayal. They go on to say that, with Captain Amagai by their side, they can finally be respected by the other Divisions. They turn to Amagai, who has already fallen asleep in his chair. Kira, walking around in the early hours of the morning, stops to examine what Kibune is doing. As Kira watches on in confusion, he releases a Hell Butterfly from his cupped hands.