Youngho stars as our protagonist of the first game. His day starts with him heading to class for his exams after pulling off an all-nighter. Along the way, he sees a girl eyeing him down and whom eventually tells him to "get lost". As he continues forward, he watches an ambulance that's wheeling off his classmate, Taehoon (whom apparently committed suicide). Along the way, he runs into another fellow classmate and friend, Seho. Seho states that a student named Myung Gil Kang bullied him into this state. Before entering the building, he finds a pendant dropped on the floor that clearly belongs to his teacher and crush, Ms. Song.
As he enters the building, Myung Gil Kang calls Youngho over. Myung bullies Youngho for a bit and tells him to stay away from a girl named Mina who is both a good friend and neighbor of Youngho. Youngho heads to class and runs into Ms. Song. She discusses that she needs to talk to him after class about his grades and the thought of mentioning the pendant slips his mind. He decides it'd best to wait after class.
As he begins his exams, his eyes begin to get heavy and he passes out. Suddenly, Youngho wakes up in a different world resembling the one he lives in. It looks like his classroom, except darker and creepier. As he looks around the building, he runs into whom looks like a deadly Ms. Song holding a sharp object. She chases him around the building as he hides and escapes from her. Not too long after, he runs into a girl named Yaesol. The two talk and Yaesol tells him the world around him is real, much to his disbelief. Yaesol asks Youngho to find the Main Building Key.
After retrieving it, he crosses paths with Seho after leaving class. Youngho tries to explain what's going on with Ms. Song, but Seho seems to not believe it. After asking Seho for his phone number, Seho states that he "forgot something upstairs" and leaves Youngho alone, yet again. Returning to the cafeteria, he talks to Yaesol yet again and discusses his meeting with Seho and still concludes that this is a dream. Yaesol attempts to convince him otherwise by telling him to head to his homeroom if he wanted answers. Along the way, he runs into Seho yet again in the bathroom. Seho claims he saw the "crazy Ms. Song" that had attempted to attack him and states that he'd rather wait in the bathroom until they can find a way out.
Youngho goes through various rooms, including the security and headmaster's room, in order to claim the keys for the school. While travelling around the school, he discovers odd secrets about the school. He also finds these weird holes within lockers that allow him to travel to places he normally couldn't reach. After being chased yet again, by the fake "Ms Song" heads towards his homeroom alone, where he finds his report card and that he's failing in 3 classes. The first one being math, which is no surprise to him. The second one is social studies, which is a slight surprise to him. And the third being Art, a class he feels is "too subjective to fail."
After checking his report card, Youngho heads towards the cafeteria yet again to meet Yaesol, but instead he runs into a man that continues to write notes on the wall. After asking the man the location of Yaesol, the bothered man begins to state where he last saw the girl and that she and the creature following have been rivals since as long as he can remember. After disclosing this information, the Message Man tells Youngho to stop bothering him so he can continue writing his notes as it is his duty.
Youngho reaches his class and meets Yaesol yet again, whom is slightly impressed he made it this far. After reviewing Youngho's report card and insulting him for it, Yaesol tells Youngho this is possibly one of the reasons he's here. (The option to fix Youngho's grade is optional, but will lead to the true ending) Youngho then heads to the basement area of the school and sees Seho yet again who is urgently looking for something. Seho becomes embraced and possessed by a demonic figure. Youngho demands the creature let go of Seho. The creature strikes a deal for both their safety in exchange for a piece of a musical Recorder that is known as a relic. Youngho sets out to find it by returning to the bathroom Seho was "hiding in" and figuring out that it's somewhere near one of the red symbols that looks like a Recorder.
Along the way, if the player so happens to choose so, Youngho changes his grades. He runs into a math student who contemplates his own failings and has stated he's been studying for an eternity. In the next room is a math equation that Youngho couldn't solve, but remembers doing so in the past. The student states he'll help him with his homework if he can get the key to the teacher "Mad Dog's" room. Mad Dog is known apparently for being an extremely strict math teacher and most people both hate and fear him.
Along the way, Youngho finds out the school has cameras set up all around the school, including the bathrooms (Much to his disgust). He eventually finds Mad Dog's key, along with other information on Mad Dog, such as the password to his old and new computer. After going through a secret passage set by a code on a computer, he hacks Mad Dog's computer and contemplates changing his grade. It is highly suggested that Youngho refuses to change his grade. He returns to give the student the key to help change his grade, and the student keeps his bargain by helping Youngho learn to defeat the math problem. After solving the equation, Youngho's math grade changes.
He also eventually runs into a shade (The proper term for these human-like creatures) of his friend/neighbor Mina Park, whom is severely injured. After asking her to stay put, he goes to the medical room and finds a medical kit. He returns to Mina as soon as he can and helps her bandage her wound. She thanks him and she disappears.
He eventually finds the part of the recorder in the biology room, where it is sitting in front of the image of two hands holding the recorder. He returns to the basement and gives it to the Shade to set Seho free, but she goes back on her word and tries to attack Youngho. However, someone repelled the Shade back and both the Shade and Seho disappeared. Now, after getting the code from a note from Ms. Noh on the instruments' cases, Youngho sets out to go to North Building.
Once, he enters the North Building, he encounters a shade-version of Myung-gil, who doesn't let him pass into the hallway and admits to killing Taehoon when he entered the North Building. If you helped Mina with her injury, she confronts Myung-gil on his bullying Youngho and killing Taehoon and leaves, making Myung-gil go after her. After he leaves, Youngho goes further into the North Building with the killer chasing after him.
He makes it to the library, where he reads a note from the library assistant, saying that they saw Taehoon go into the media room. He gets the media room key from the desk and goes through obstacles to the media room.
If Youngho goes to the art room during his journey, he finds that the reason he is failing the class is because he didn't submit a drawing of Ms. Song in because he thought it looked stupid. He remembers he left it in the classroom and decides to go find it.
Once he enters the media room, he gets scared by a random video appearing on the projection screen and finds a bloody video cassette tape, which had "Secret" written on it. It turns out that Taehoon left it behind before he was murdered by Myung-gil, so Youngho was resolved to see it through for Taehoon. He goes to the headmaster's room in the Main Building and uses the secret room to view the tape, which shows the Shade opening a secret room in the library and that the killer was leaving the room as Ms. Song.
When Youngho goes back to his classroom, he gets his artwork of Ms. Song and admits that it didn't look half-bad from a different perspective. If he turns in his artwork, his grade improves. If he doesn't, then it will fail.
He goes to the first library floor and goes into the back hallway to swipe the same books that the Shade threw in the video as it opened a secret door. Once he entered in, he saw a mannequin wearing Ms. Song's clothes and wearing her pendant that Youngho found earlier this morning. It turned out that dressing a mannequin with the person's clothing and items was how the Shade was controlling her puppet, the killer. After he took the pendant, he saw the picture of the young girl he had since he entered the Coma fit perfectly inside of Ms. Song's pendant. It was then, the whole school shook tremendously and he started running to escape the collapsing school. However, the killer appeared before him and tried to attack him, but Yaesol intercepted and blocked the killer, allowing Youngho to escape.
If Youngho was honest during the game in telling Ms. Song about Myung-gil's bullying, telling Yaesol about his report card, helping Mina with her injury, and deciding not to change his grade in Mad Dog's computer, he can meet The Noteman again on the third floor of the Main Building. He asked The Noteman about the Shade, which he said that he was a shade and that they were beings born in the Coma. When Youngho asked why she was angry with him, The Noteman said it was probably because he was a trespasser, which he also dislikes. When he asked about picture of the young girl, he answered that she was a Ghost Vigilante that was in the Coma long ago and was Ms. Song's past relative. When Youngho asked why the Shade dressed the killer as Ms. Song, he said it was probably to spite the girl in the picture to dress the killer as their own descendant. Then after he asked how to leave the Coma, The Noteman said to go back when it all started, which was in his classroom.
After getting back to the classroom, he can get many endings based on how many grades he changed and whether he was honest or not.
Ending 1: One Objective Cleared
He goes inside the classroom to see that the vines were gone and the classroom looking normal. When he leaves through the other door, he remarks on saying he was glad to be out of the Coma. However, the Shade comes up beside him with a sinister smile saying, "I wouldn't say that." In the normal world, a bunch of students are outside near an ambulance, talking about how a freshman was having a seizure in front of his class and he was going to the hospital. It turned out that it was Youngho. After a couple of students were making remarks to Myung-gil about he was going to be in trouble, he tried to dismiss the claims in front of Mina, who told him to shut up and was worried about Young-ho. After the ambulance leaves, it shows Yaesol standing against the wall and was disappointed that Youngho didn't escape in time and that the recorder relic is still in the Shade's hands.
Ending 2: Two Objectives Cleared
The ending is the same as above, it shows Ms. Song tries to get inside the ambulance to go with Youngho, but the paramedics told her that his parents were on their way to the hospital and that she needs to take of her students. Once they start leaving, Seho, who was standing Ms. Song, says that Youngho will be fine and she says, "I sure hope so.".
Ending 3: Three Objectives Cleared
With the first and the second ending combined, the third ending shows a scene of Ms. Song looking her pendant wondering why Youngho has her locket when he was having a seizure in class. After that, she said that she'll need to talk to her grandmother, which is the picture in the picture.
Ending 4: Honest Heart
Before he enters the classroom, he encounters Yaesol, who congratulated him on escaping the killer and told him that it turned out that Seho was switching his work with Youngho's, meaning that Youngho was originally one of the top 3 students instead of Seho. Once she tells him t go inside, she remarks that only one can go. After that, it shows Mina at the hospital, where she is visiting a hospitalized Youngho. It turns out that Mina is holding Ms. Song's pendant in her hand and wonders why Youngho was holding it. While she leaving the hospital, she passes by Yaesol, who was in her casual outfit instead of the school uniform, and MIna wonders if Yaesol knew Youngho. Mina decides to get to the bottom of the mystery and help Youngho as Seho lurks and watches Mina from the bushes.