Keitaro and his childhood sweetheart make a promise to be accepted at and to meet each other at the prestigous Toudai University before she moved out of his life. About a decade later, Keitaro has become an artist and a daydreamer, having ranked 27th from the last in the national practice exam. When his grandmother leaves the all-girls dormitory, he becomes the residential manager and soon meets up with two Todai applicants who may have been that sweetheart, since he`s forgotten her name. Then there the other tenants like young Shinobu who was in despair until Keitaro helped her, Motoko the swordsmaster who sees men as evil distractions, Su Kaolo the genius child inventor and the sneaky Kitsune.
The unlucky Keitaro is given a break when his grandmother asks him to be the manager of Hinata Inn. Keitaro accepts but little does he know that since he's last been there, the inn's become a girls' dormitory! None of the tenants are all too happy about a male living with them until they begin to believe that he's a student of Tokyo University.
Shinobu's parents are getting divorced and she doesn't seem to have many friends at school but Keitaro and the girls welcome her with open arms which leads her to decide to stay at the inn instead of living with either of her parents.
The master of the sword, Motoko, returns from a training retreat only to find that Keitaro has been named the manager of the inn. She's outraged and is completely against a male being the manager but becomes confused by weird feelings that consume her body. Could it be love?
The girls discover that Keitaro is not really a Tokyo University student and to make things worse, his studies don't seem to be going very well. Seeing this, Keitaro decides it's time to leave Hinata Inn.
It's time for the exams for Tokyo University, and unfortunately, both Keitaro and Naru fail. Disappointed, they go their own separate ways to take a break from Hinata Inn. Or do they?
After finding out that both Keitaro and Naru are in Kyoto, the rest of the girls at Hinata Inn assume they're going to commit double suicide and go after them. Meanwhile, Keitaro and Naru help a girl named Mutusmi get back home which is located on the other end of Japan!
Keitaro scores two tickets to Neverland and plans on asking Naru to go with him for the grand opening. However, a new face appears and his name is Sakata Kentaro. He's richer, better looking, and smoother than Keitaro. He also has tickets to Neverland. Things don't look so hot for Keitaro.
During meditation, Motoko enters a dreamworld where everyone is living in an RPG. Keitaro is a knight on a quest to save Naru from the Dragon King and the silliness of it all turns off Motoko. But as she continues to meditate further, she finds a lesson in the dream.
A thief has stolen the rent money of Hinata Inn and everyone panics. That is everyone except Detective Kitsune and her sidekick Kaolla Su. The cast begins to assemble the clues and attempt to solve the mystery of the missing rent money.
A mysterious woman appears in Hinata with her pet alligator. The duo are wreaking havoc all across town and Kentaro claims that it's actually a grown-up version of Kaolla. Is it?
Naru becomes a celebrity all across Japan as an idol and this, of course, leads to Keitaro worrying about her studies. He begins to believe that Naru no longer cares about getting into Tokyo University and becomes incredibly depressed.
When Motoko runs out of clothes as they're all in the laundry, she is forced to wear a dress. Furthermore, her swordsmanship has been foiled by not only Tama-chan but also Keitaro. This leads her to doubt herself and things get worse when Mecha Tama-chan begins to create havoc.
After witnessing Keitaro almost kiss Naru, Shinobu wonders what a kiss is like. Supposedly, it tastes like a lemon and is as soft as a marshmallow and thus begins Shinobu's quest for her first kiss.
Hinata Inn is having a financial crisis and everyone must take up a part-time job. When Keitaro becomes an assistant for Naru's first love, Kitsune becomes incredibly worried and curious at the same time about what might happen when Naru discovers that Seta is back in town.
When Keitaro has to take care of Seta's adopted daughter, Sara, Naru of course finds out about Seta. Keitaro begins to give up his hope of Naru ever liking him and decides to help her be happy instead.
The tenants of Hinata Inn are working part-time at a beach tea house and decide to perform a play to increase revenue. Keitaro is still incredibly glum about the whole Seta and Naru situation and it's pretty understandable.
Naru becomes possessed by an evil spirit and Motoko is the only one who can destroy it. Unfortunately, she doesn't know the technique to kill the spirit without killing the body and it's quite a predicament.
Seta has to leave on an excavation trip and asks if Sara can stay with the girls at the inn. Sara doesn't take too kindly to this and decides to run away while causing as much trouble as she can to everybody else.
A man who happens to look exactly like Keitaro when he wears glasses appears and is later found out to be from Kaolla's home country. He is here to get married to Kaolla but she decides she isn't quite ready yet, but tradition says she must.
Keitaro discovers a doll that can move on its own. Everyone is amazed by it but Keitaro seems to be able to hear it talk also. He finds out from the doll that his great grandfather promised to fix its legs but never did and being the good guy he is, Keitaro decides to fulfill his ancestor's promise.. With the help of the girls, of course!
Naru and Keitaro decide to go out to celebrate the latest grades and while both are wondering whether it's a date or not, a mysterious little girl appears.
Mei is Naru's stepsister and hopes to take Naru back home. To accomplish this, she decides she has to hook Keitaro up with Mutsume and it is in this episode that Naru finds out something shocking.
Naru now wonders what she should do with her newfound knowledge and it seems like Keitaro is going to be returning home since his grandma has returned to reclaim the inn. To add more to the mess, it doesn't look like Keitaro's studies are going to be enough to help him into Tokyo University.
The final episode of Love Hina. Everyone has to leave Love Hina for a day because the inn is going under renovations. It also becomes apparent that Keitaro won't be coming back to Hinata Inn and Naru has completely given up on Keitaro. Who will Keitaro decide to be his soulmate, Naru or Mutsumi?
Out of nowhere, Motoko's sister appears and is ready to pass on the dojo. However, Motoko is still not quite as strong as her sister and when big sister finds out about this, she gives Motoko an ultimatum: Motoko must beat her sister or marry Keitaro!