En Honoka is one of the twenty-two identical clone sisters known as the Honoka sisters, created to serve as Guardian pilots for the seed ship Sidonia. She is designated as the oldest among them and pilots unit TS203 or TS703. Like her sisters, En possesses a slim build, stands fairly tall, and has light pink hair styled in a hime or princess cut, paired with brown eyes. Although her chronological age is approximately five years old, she has undergone accelerated growth and compressed mental training to fulfill her combat duties.

En is introduced as a trainee pilot with a notably aggressive and resentful disposition, particularly toward the protagonist Nagate Tanikaze. This hostility originates from a misunderstanding when she mistakenly believed Nagate was spying on her and her sisters in their changing room, leading her to physically attack him. As the narrative progresses, En participates in a critical mission alongside Nagate, Kunato, and Shizuka Hoshijiro to retrieve a powerful weapon called a Kabizashi from a previous battle site. During this operation, she is incapacitated and subsequently falls unconscious for an extended period, remaining in that state from an explosion during a battle against a Chained Gauna until a later confrontation with an Asteroid hiding Gauna.

Upon regaining consciousness, En continues to harbor her resentment toward Nagate, demonstrating a long memory for perceived slights. Her animosity is further underscored when she attacks Nagate after he inadvertently interrupts her and another sister, Ren, while they are engaged in photosynthesis, a biological process likely related to their cloned nature. Despite this lingering anger, En, along with Ren, is suggested to develop romantic feelings for Nagate, adding a layer of personal complexity to her interactions with him. Her core motivations evolve from proving herself as a capable pilot and defending Sidonia from the extraterrestrial Gauna to navigating her personal grievances and emerging affections for a fellow soldier. Key to her development is the relationship with her sister Ren, who comes to trust Nagate and actively seeks to mend En's fractured relationship with him. Other notable relationships include her comrades in arms, such as Kunato, with whom she served on the retrieval squad.

As a pilot, En's notable abilities include operating a Guardian in high-stakes combat missions against the Gauna, the primary antagonists of the series. Her role in the story is that of a supporting character whose personal vendetta and subsequent gradual shifts in perspective highlight the interpersonal conflicts among Sidonia's defenders. Through her journey from an irate accuser to a potential ally emerging from a long recovery, En Honoka contributes to the series' exploration of duty, memory, and the bonds formed between engineered soldiers fighting for humanity's survival.