Before going down the newly-revealed staircase, take a right turn and follow the short path down the hall. Upon making a left turn, you should see some rubble that blocks the path. Hidden Monokuma #1 floats on a flying saucer above the rubble. Go down the stairs and smack rubble away whenever it blocks the path (they should be marked with a 0, meaning that Shuichi doesn't have to bond with anyone to clear them). Open the door at the end of the path to enter the Ultimate Supreme Leader Lab. Examine the book on the floor to the left. Maki will then arrive to discuss the History of Hope's Peak with Shuichi. After another scene, Shuichi's Friendship Power increases to 1, thanks to Maki. Examine the showcase, central chair, emblem, shelf, helicopter, supercar, and helicopter controller in front of the car. Shuichi gathers that this seems more like a child's idea of an evil organization than the real thing. Exit to the next area.
Outside the Academy
Smack the rocks away at the entrance to exit the school building. Go to Kokichi Oma's Room to continue the investigation. Inside, examine the box of documents to the right, the collected evidence to the left, and the Kubs Pad on the bed for Kokichi's Motive Video. Speak to Maki to discuss the Killing Game itself. Exit after investigating everything and follow the right path to the Backyard spot where the manhole is. Along this path is Hidden Monokuma #2, flying around over the field on a rocket. Enter the Backyard and examine the writing on the wall to the left; Shuichi is now left with Two Mysterious Messages. After the scene, Shuichi obtains the Keebo Gun, allowing him to absorb energy from Exisals to summon Keebo. Return to the school.
Upon entering, use the Keebo Gun to get rid of the Exisal blocking the path to the left. Go upstairs and follow the path to debris marked with a 1. Keep going to the fourth floor (taking out the Exisal with the Keebo Gun in the hall here) and then the fifth floor. Pick up Hidden Monokuma #3, dancing on the railing above the stairs, and clear the debris down the hall to gain access to the Ultimate ??? Lab. Examine the laptop on the table and the giant vault at the back of the room. Examine the giant vault again to operate the dials based on the messages left behind by Kokichi: turn the left dial to the Gemini sign ("twins b") and turn the right dial to the horse ("horse a"). Examine the vault again after it's been opened to find a USB stick. Examine the laptop to view Rantaro's Video Message. After the scene, Shuichi's Friendship Power will increase to 2, thanks to Himiko. Exit the room and Tsumugi will approach to tell Shuichi about a new room.
Return to the school's first floor and take a left from the stairs to find debris labeled with a 2. It can now be cleared, so smack it away to proceed down the hall and gain access to the other hall, past the gate. Take out the Exisal and go through the door with the checker pattern on it. Halfway up the spiral stairs is Hidden Monokuma #4, dancing on the structure in the center. Enter the Ultimate Astronaut Lab at the top of the stairs and enter the new room through the large hole to the right. Wait until the cutscene ends and then examine the documents at the center of the room to find the Gofer Project Participants List. Shuichi's Friendship Power then increases to 3, thanks to Tsumugi. Exit and return to the entrance hall.
Summon Keebo to get rid of the Exisal in the entrance hall and approach the debris past it, labeled with a 3. Smack it away and take the stairs down to the basement. Enter the Library to find Maki. Speak to her to learn about the Bugvac. Speak to Himiko after she enters and then examine the moving bookcase to the left. Examine the hidden room after Keebo opens it up to enter. Examine the curtain at the back of the room to reveal the Motherkuma. Examine the Monopad on the table and the trash can to the right. Inside the trash can is a Shot Put Ball with Pink Fiber. Speak to Himiko for some Clues to the Mastermind and the half-broken door for the Hidden Door in the Library. Exit for a scene and then examine the hidden room again to max out Shuichi's Friendship Power. Go to the second floor to use it.
Smack away the debris labeled with a 4 to gain access to Classroom C. Smack the pile of desks and chairs away to reveal a hologram display on the floor. Examine it and when given the opportunity, open the locker. This provides the Flashback Light Settings Bullet. Speak to Himiko after she arrives and she'll direct Shuichi to the Girls Bathroom on the first floor.
Speak to Himiko outside the Girls Bathroom and then enter. Examine the utility closet and go down the secret passageway to the Hidden Room for the Hidden Room Passageway Bullet. Examine the Motherkuma and then speak to Himiko to conclude the investigation here. Return to the Girls Bathroom and then exit to the Courtyard for a scene. Go to the Shrine of Judgment one last time for a trial.