Mad Father has a total of three Main Endings, and two Bonus Endings.
Bad Ending 1
In the first bad ending, Aya has to Grant Mom's Wish and let her take Alfred with her at the end of the game, when the player has gone through the cursed Mansion. The ending scene shows Aya all alone in the room, since Monika has taken Alfred away. Aya then proceeds South, and tells Maria, who seems to have not recovered from a shock. In the next slide, Aya and Maria are in the Shrine, paying their respects to her parents. Aya is about to tell Maria she can stay with her when the assistant suddenly lunges at her. The screen blacks out and a scream is heard. The next frame shows Aya on an operating table, blood pooled under her, with Maria stating that she will continue to take on the doctor's work.
Bad Ending 2
The second bad ending, consisting of Aya continuously ignoring Maria. The player is to ignore Maria throughout and proceed through the game as usual. Towards the end, when Monika appears, choose to Save Father.
Gem collection does not affect this ending.
Aya's mother then fades away, upset by the decision Aya has taken. In a frame after that, Aya goes through a flashback which shows how Alfred cheated on Monika, and was planning to make Aya a doll. Alfred also killed Monika when she found out. Maria, being loyal to the doctor, did not mention this to Aya. In the next scene Aya wakes up near Alfred in the laboratory and is terrified. Alfred then reveals how he believes in 'preserving the beauty and innocence of children' by turning them into dolls. Aya then has to run for her life. She runs to a small mortuary, and hides among the corpses. Maria arrives searching for her. When Alfred finds out that she lost her, he then proceeds to wound Maria's leg with his chainsaw. Aya ignores Maria, runs to the Shrine, trips over a doll and is soon caught by Alfred, who then proceeds to kill her.
The next scene shows Aya wearing a red dress and sitting in the throne of the Doll Room. Alfred walks in, tells her that she is beautiful, and says goodnight to his precious doll.
The canon ending of Mad Father, consisting of Aya paying attention to Maria. The player is to search her for her key, backtrack to the Archives, go to her room and read her diary. The player must then proceed as usual. Towards the end, when Monika appears, choose to Save Father.
Monika will fade, and Aya will see the same flashback from Bad Ending 2. When Alfred reveals his intentions, Aya must run towards the Morgue, and hide among the corpses. When Alfred betrays Maria, Aya must find the Bandages located on a bookshelf, and treat Maria's wounds.
They will escape together, until Maria trips and tells Aya to escape without her. Alfred will then catch up, kick Maria aside, and chase Aya into the Shrine. When Alfred attempts to kill her, he is stopped by Maria, who throws knives at him. Believing him to be dead, Maria then confronts Aya and tells her that she had no choice.
Just then, Alfred attempts to kill them both, but is then killed by Dio, who stabbed him with a pitchfork. Aya then passes out from the shock of what just happened. When she awakens, Dio then explains that he must burn down the Mansion to prevent history from repeating itself. Dio reveals that Monika told him to protect them, and then proceeds to kiss Aya's forehead, saying, "Goodbye, Aya. May you be smiled upon." This is a reference to a good luck charm that Monika gave Aya when she was young.
Maria and Aya then flee the burning Mansion. The scene then cuts back to the Shrine, where Ogre persuades Alfred to perform experiments in Ogre's dimension. It is then shown that Aya and Maria are leaving the Mansion, when Maria stumbles upon a mysterious book. Aya then catches up with Maria, and then Maria is shown looking at the moonlit sky.
Years later, Jean Rooney visits a Medical Clinic owned by Aya, due to her doctor refusing her because of her lack of money. Aya then tells Jean that she accepts patients for free, leads her to a patient table, and gives her a sedative. It is then revealed that Aya is continuing her father's work, and Maria comments to herself that it must run in the family.
The End Credits roll.
A bonus scene after the credits of the True Ending. It can be unlocked after you collect all 21 gems. If you need help finding these gems, use this guide. While searching for the gems, make sure you complete the steps necessary to get the True Ending, and then proceed as usual.
After the credits roll, Alfred is seen gazing upon a more mature version of Aya. Ogre walks in, congratulates him on his work, and states that he wishes for the Aya clone to explore Alfred's dimension.
It can be noted that this could be a connection to the game's predecessor, Misao, as Alfred's hair is a slight shade of purple, the same hair color of a similar psychopath in Misao. In that game, there is a girl named Miss Library; her appearance and personality sharing similar traits to Aya, and key items from Aya's room can be found in Library's room, such as her Diary, her childhood books, and a picture of Monika Drevis.
The last (and most obvious) connection is Ogre, who's appearance and personality are the same as Mr. Onigawara, the Save Point in the game who disguises himself as the Student Council President.
The second bonus epilogue in the game, which is unlocked after all the Gems are found, and the Gems Ending is found. Once this is complete, simply access the Gallery via the Main Menu, and then select "if."
The scene begins where Dio saves Maria and Aya from Alfred, to which Aya passes out from shock. They are then taken Aya's room, where she is sleeping. Dio then tells Maria about Monika's wish, and treks her that she must leave the Mansion with Aya. Dio then decides to explore the Mansion for a while.
If Dio decides to travel towards the Bathroom, he is then greeted by the Old Man, who is bathing in blood. The Old Man then reveals that he was taken to the Mansion as a servant rather than a test subject, and claims that Monika brainwashed Alfred. He tried to run away, but was quickly killed by Alfred. It is then revealed that Dio was also a servant, but Dio then states that he trusts Monika, to which the Old Man responds, "Hmph. Well, what do I care, I suppose?" This is a reference to what he mumbled to himself when Aya interacted with him.
If Dio decides to go to the Cafeteria, he is then meet by Ogre, who is sitting at the table drinking tea. It is then revealed that Alfred burnt Dio's face, but Ogre saved him using an unknown medicine. Ogre then states that he was watching the whole time, and was amused by the series of strange events, much to Dio's surprise. When he asks what his goal is, he then reveals his demonic form, and states that he just enjoys seeing and/or watching deranged humans. He then states that good people like Dio are created to help lunatics flourish. Afterwards, Ogre vanishes.
After these events happen, Dio walks out and sees Maria and Aya prepared to leave. He then approaches them, to which Aya reacts by blushing and running off. Maria apologizes and states that Aya is just shy.
Dio then tells Aya about her mother's wish, and proceeds to burn down the Mansion, just like in the True Ending. After they leave, Dio steps outside, revealing that he is not one of the corpses. A doll appears from behind a tree, and asks if Dio will follow them, to which he declines, stating that they would hate him if they did, and that he would become a burden. The doll then asks him what he would do if Aya followed her father's footsteps, to which he states that he would try to stop her, no matter how futile it would seem. The curse fades, and Dio walks away.
The rest is left ambiguous.