The story begins with Rito rudely awakened by each Deviluke alien. Rito explains his routine life and is most concerned with Momo due to her deceptive intents. As Rito arrives to school, he meets Haruna. Lala tries to encourage Rito to confess to her, but Rito pushes Lala to a corner and explains to her the situation is complicated as people are legally allowed to marry one person. Out from nowhere, Celine clings onto Rito. Momo and Nana surprise everyone that they have enrolled in their school. Now students, Momo winks at Rito, reminding him of the conversation last night in the bathtub. Momo overheard Rito's concern about marrying multiple girls and explained to Rito that many girls love him and marrying them all would make everyone happy. As the future king of Deviluke, he can have many concubines. Momo vows to create a harem for Rito. During class, Momo becomes popular among the boys while Nana greets a mysterious girl looking out the window. Nana impresses her with her ability to understand animals. The girl introduces herself as Mea. Later, Momo finds Yami at a bench. As Yami is an obstacle to her harem plan, Momo tries to secretly enlist Yami in her harem plan by convincing her to enroll. The conversation gets cut short when Rito runs in panic stating that the other boys suddenly went violent. The other boys arrive on the scene and attack Yami, forcing her to use her weapons. After Yami and Momo restrain the boys, Yami hears a mysterious voice reminding her that she's an assassin assigned to kill Rito.

Mea speaks with the mysterious voice about her day. The voice reminds Mea about her job; killing Rito and reverting Yami back to an assassin. Meanwhile, Momo warns the dangers of Yami to Rito and convinces him that Yami may change back and kill him anytime. Next, Momo is surprised to see Mikan invite Yami over for cooking lessons. Nana also comments about making a new friend to Lala. During the dinner service, Rito freaks out over Yami's Taiyaki soup and thinks she may have set a trap. He nearly vomits and asks to go shopping. During bedtime, Rito finds Momo in his bed. Momo warned Rito earlier that she must protect Rito to allow the harem plan to progress. Yami may kill Rito in his sleep. As Rito tries to sleep, Momo caresses him every way, forcing Rito to shove her aside. As Rito later takes a drink, Yami asks Rito for a talk. Yami explains about her cooking lessons and compares it to her attacks. Momo mistakens it for an assault and jumps down to defend Rito. Yami only wanted to know if Rito enjoyed her Taiyaki soup. The next day, Yami also becomes enrolled. Mea finds with Yami and explains how she is Yami's sister with similar abilities. During class, Yami does not get along with other students and blocks people from befriending her. Momo offers to help but get rejected too. Meanwhile, Mea asks Nana about Rito. Nana simply replies, "He's a beast." Her rambling comments about Rito only interests Mea, who then goes to find Rito herself. Momo then talks to Mikado-sensei, who loved Yami being enrolled. She tells Momo how Yami's lifestyle has been nothing except fighting. While Yami is sitting on a bench wondering about her feelings Yui approaches Yami and tells her that not understanding their own feelings is normal, and she too does not understand her own feelings. Then Nana asks Yami if she's seen Mea. While Rito is asleep on the roof Mea climbs on top of Rito and whispers how she'll be able to know what he's truly like once they are "joined together".

Rito wakes up and finds himself inside his bathroom with Mea. Mea tests Rito's beast-like moves and asks Rito if he experienced something similar. She reads Rito's memory about Momo and her harem plan. Yami cuts Mea off from reading Rito's memory and warns her to not bother Rito. Mea walks off and learns about the harem plan and how she and Momo are competing for Yami. Later, Nana introduces Mea to Lala and friends. Rito sees Mea and realizes her from the dream earlier. As Mea speaks obscenity to Rito, Momo considers adding Mea into her harem plan. Afterschool, Rito spots Yui and offers to walk home together since Mikan is cleaning up Saibai's atudio and Momo and Nana are with Lala at an important event. Yui is first skeptical but accepts. Momo secretly escapes from the event, a Magical Kyoko Costume Show, and observes Rito walking home with Yui. She finds this a perfect opportunity to advance her harem plan and devises a way to lure Rito and Yui into Rito's house. She first uses the princpal to chase them toward Rito's home and simulates rain to get both of them inside. Inside, Momo surrounds the home with a barrier and creates a romantic scenery by simulating rain and a blackout. Rito accidentally falls onto Yui, giving Momo signs that her romantic scenery is working. Her patience runs out when she finds Mikan and the others trying to get inside. Then, Mea shoots a laser beam and destroys the barrier, breaking Momo's scenery and exposing Rito and Yui to everyone. Lala tells Rito there was no rain today and Mikan sees Momo's tail, adding to her suspicions about Momo. Meanwhile, Mea tells master she was only messing with Momo's harem plan.

The vindictive Azenda the Tyrant comes to Earth to provoke Yami. Later, Haruna and Rito have yet an awkward encounter, and Mikan and Yami grow closer.

Rito dodges potential encounters with women -- and all their respective parts! -- but he soon gets a firsthand look at the female anatomy... and not in the good way.

Momo teaches Rito about the secrets of the female body and seeks to move Project Harem forward. Meanwhile, Rito learns about Ren and Run.

As Lala fixes up Nana's De-Dial, Momo tells to Nana grow up while looking at her chest, infuriating Nana. Lala brings out an item that grows Nana's breasts, but it only works for a few seconds and shrinks Momo's breasts. Momo sarcastically admits that she understood Nana's feeling. Later in Mikado-sensei's office, Rito and friends discuss about Lala's inventions and Oshizu asks about Lala's childhood. Momo recalls the frequent incidents with Lala's inventions; whenever she was fighting with Nana, Lala's inventions ran wild and they both cleaned up Lala's mess. At lunch, Rito and friends visit Mea's apartment. The apartment is empty and Mea notes that she lives alone. Nana finds it strange knowing that Yami is her sister while Momo was hoping to collect more details about master. In the follow-up meeting with Mikado-sensei and Oshizu, Momo expresses concerns about Mea and how she may be hiding her true heart. Yami notes that their hearts are incomparable with a human's heart because she and Mea are both weapons. Rito invalidates Yami's claim and relates the sibling analogy to Mikan. The meeting is cut short when a dog clings onto Oshizu, making her rip Yami's clothes, causing Yami to chase after Rito. Afterschool, Ren gives Rito Run's CD and explains about Lala's pure sweet child personality. Rito considers it as he thinks about Momo's harem plan. Later at night, Mikan asks Rito to call Lala and her sisters down for dinner. Rito enters Lala's room and finds her fixing an invention. Rito asks Lala when she started making inventions; Lala replies that it naturally came to her whenever she got bored. Momo hears Rito in Lala's room and thinks Lala is about to kiss Rito, but rejects the theory. She and Nana listen on. Rito asks Lala about her incidents; Peke replies that they were incentives to reunite Momo and Nana. Remembering what Ren said, Rito panics as he looks at Lala and activates an invention, tying both of them up. Momo and Nana discuss how much Lala cared f

Rito begins to get closer with Momo, which makes Mikan uncomfortable. After Rin helps her during a near collapse while walking home, Mikan can no longer hold her tongue.

That Lala and her inventions. One of Lala's crazy contraptions ends up getting Rito and Yami stuck to each other by their hands!

The truth needs to come out. Yami finally begins telling Rito about her past, and explains how she came to be.

The Organization is on the move and Yami is the firs target! Meanwhile, Lala learns of a new enemy that may be closer than she thinks.

Momo takes to playing dating sims to figure out how to get her harem under way. At school, a group of students form a Momo fan club, which ends up keeping her away from Rito.