On the night of the Tanabata festival, a shy and socially awkward young man named Tsuyoshi Yamada is riding the train home to his small, cluttered apartment in Tokyo. An otaku whose life revolves around anime, video games, and online forums, Yamada keeps to himself, finding comfort in his hobbies rather than the complexities of the real world. On this particular evening, a beautiful and elegant woman named Saori Aoyama is being harassed by an old drunkard on the same train car. Despite his crippling lack of confidence, Yamada is the only passenger who musters the courage to intervene, confronting the man and escorting him off the train at the next stop.

Deeply grateful, Saori thanks him, and a few days later sends him an expensive gift: a pair of Hermès teacups. Yamada is stunned. He has no experience with women and is completely at a loss for what to do next. Desperate for advice, he turns to the anonymous community of an internet message board, where he posts an account of what happened. The board's eclectic members, a collection of lonely hearts, tech geeks, and social misfits, are electrified by his story. They give him the nickname Densha Otoko, or Train Man, and begin to offer a constant stream of encouragement, strategies, and often contradictory dating advice.

The narrative follows Yamada as he tentatively begins to court Saori, whom the forum members nicknamed Hermès after her gift. Every phone call, text message, and date is meticulously reported back to the board, where his online friends celebrate his small victories and console him after his awkward blunders. Their investment in his quest becomes a catalyst for change in their own lives, as many find the courage to confront their personal challenges. As Yamada, a clumsy and stammering buffoon who frequently collapses under pressure, stumbles his way through a world of fancy restaurants and unfamiliar social etiquette, he slowly begins to emerge from his shell. The central conflict arises from his fear that Saori will reject him if she discovers his true otaku nature, forcing him to reconcile his beloved hobbies with his burgeoning adult relationship.

The series is set against the contrasting backdrops of Tokyo's high-society locales and the neon-lit, figurine-filled shops of Akihabara. Notable narrative arcs include Yamada's disastrous attempts to appear sophisticated, the forum members' parallel struggles and triumphs, and the emergence of a rival suitor, a handsome and successful businessman who seems a far more appropriate match for Saori. The story builds toward a final, public declaration of love, where Yamada must prove that the courage he found on the train was not a fluke. The television series features an extra episode, Another Ending, which focuses on the background lives of the message board members, and concludes with an eleventh episode that resolves the central romance.