"Me and the Alien MuuMuu" centers on the unexpected encounter between a high school student, Takuya, and an alien named MuuMuu, who crash-lands on Earth. MuuMuu, a small, blob-like extraterrestrial, possesses the ability to transform into a humanoid form resembling a young girl. Despite her alien origins, MuuMuu is curious and naive about Earth's customs, often leading to comedic misunderstandings. Takuya, initially reluctant, becomes her caretaker and guide, helping her navigate human society while keeping her true identity a secret.

The narrative explores their daily lives as MuuMuu attempts to blend in, often causing chaos due to her lack of understanding of human behavior. Takuya’s friends, including his childhood friend Yuka, gradually become involved in the situation, adding layers of interpersonal dynamics. Yuka, in particular, grows suspicious of MuuMuu’s origins, creating tension as she tries to uncover the truth. Meanwhile, a government agent, aware of MuuMuu’s presence, begins investigating, adding a sense of urgency to the story.

Themes of friendship, cultural exchange, and the challenges of coexistence are woven throughout the series. MuuMuu’s interactions with humans highlight the differences between Earth and her home planet, while Takuya’s growing bond with her underscores the importance of empathy and understanding. The plot balances lighthearted humor with moments of tension, particularly as MuuMuu’s presence threatens to be exposed. The series concludes with a resolution that emphasizes the value of connection across differences, leaving the characters’ futures open-ended but hopeful.