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In the story, Aiko and Punpun have recurring nightmares that offer intense foreshadowing and insight into their troubles. The series itself also has strong themes of unreality and delusion.

Aiko's Dream Edit

In middle school, Aiko describes a recurring dream to Punpun, where she is waiting for someone in front of a waterfront for years. Finally, she glances someone who she thinks is her birth mother and runs towards her, only to realize it is her own reflection in the water. She always wakes up feeling lonely and worries she will carry that sense of loneliness to the grave. Instead, she can die happy only after she finds one person who can truly love and understand her.

After wrapping Mitsuko's dead body with duct tape, Aiko dozes off into a nightmare. She is in a nonsensical high school class, struggling to hold her bladder since the washroom all the way across the lake. On her desk is scrawled, "The one who sits here will be cursed with bad luck." She ends up peeing through her skirt and onto the floor, and a bloody Mitsuko appears beside her desk. A compact mirror on the desk shows Aiko's distorted reflection, and across the bridge, in the lake, Aiko sees the same reflection. This nightmare repeats many times after she and Punpun run away, and due to this, Aiko becomes upset whenever she has to fall asleep or wake up alone. When they finally reach Kagoshima, only to discover that the town has been abandoned and there is no hospital, she sees her distorted reflection in the lake, identical to her dream. She wonders aloud why she feels so lonely as of late. She decides she wants to turn herself into the police after a nap. She and Punpun find an abandoned house to rest at, and Aiko remarks that her dream of being loved by Punpun finally came true, and she's never known such a happiness. She falls asleep. Punpun wakes up to find that she has hung herself.

Aiko's reflection of the lake is a constant reminder of the loneliness and misery she wants to escape. After being reminded of that feeling in Kagoshima, she finds the moment of closeness she's been searching for and ends her life on that note, ensuring she will never feel lonely again.

Punpun's Dream Edit

Punpun has a recurring dream of watching Aiko at a distance at Cape Kadokura. When he and Aiko finally make it to Kagoshima Prefecture in real life, they visit Cape Kadokura, and Punpun instantly recognizes the beach and tower that was in his dream. He watches Aiko enjoy herself in the sand and water and returns to his bird form for the first time since Mitsuko's murder. In a good mood, he thanks Aiko for being in his life. The bliss is shattered when he finds a stray rope and plots to kill Aiko then himself, snapping back into his horned form.

Upon seeing scenes from their respective nightmares, both Aiko and Punpun realize the hopelessness of their situation and seek permanent escape, whether successfully or unsuccessfully. Since both their dreams were first had long before Mitsuko's murder, the transfer of dreamt scenes into reality could indicate the inevitable outcome of a relationship doomed from the start, only founded on escapism, obsession, and delusion.

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Reality vs. Sleep Edit

The series as a whole has a surreal, dream-like feel to it, from the mood-based physical forms of Punpun, to the caricatured features of Hiromi Numata and Yagami, to the often extreme conversations and situations characters find themselves in. There is also the repeating motif of the night sky and desiring its freedom, from Punpun's childhood wish for wings, to the Pegasus Ensemble's quest to ascend into space, to the stars of the milky way and Punpunia. After finally getting the girl in the most disastrous way possible, Punpun tells Aiko he wishes to have never wished upon that sky in the first place.

The series' title drops, "Goodnight, Punpun," are always followed by a timeskip, showing how Punpun has matured after traumatic experiences with life's harsh realities. He has trouble sleeping after Mitsuko's murder and tells Aiko, "I'm scared... I'll wake up from my dream if I fall asleep," indicating he is not ready to cope with the reality of their situation. Some characters seek to protect their loved ones from reality, in the way Punpun tells Aiko to let him do all the thinking, and the more straightforward quote from Seki towards Shimizu, "You don't need to face reality. I'll take care of it in your stead."(chapter 94) On the other hand, Sachi wishes to use her art to inspire others to fight and bend reality, rather than escape it. Several characters mention or commit suicide, seeking peace from permanent sleep. After Punpun kills God by stabbing out his own eye, he lays down and says goodnight, only to be interrupted by Sachi. She doesn't allow him to spiral any further from this traumatic experience and forces him to wake and continue living. Aiko's last appearance is in a dream of Punpun's, in which he admits her memory is already slipping away and he now aims to live and die quietly. Without Aiko to keep him dreaming of a dangerously impossible life, Punpun ultimately learns to cope with reality through a specifically calm sense of resignation and detachment.