I've decided to use screen caps extensively, as that is often the only way to convince skeptical readers of the veracity of one's arguments. Note that I use evidence from the official manga as well. Sadamoto is the character designer of the series and was involved with it from its earliest planning stages. It would be absurd to dismiss his authority on the characters as being less than Anno’s.
I have come to the conclusion that Pen Pen’s sexual/romantic interest lies solely with humans, perhaps because he was raised in their company. Not once in the series is he shown flirting with a member of his own species, or even interacting with them in any manner. Pen Pen is probably bisexual, exhibiting a strong interest in both Shinji and Misato throughout most of the show. Although he experiences some attraction with Asuka and Hikari, Misato and Shinji constitute his main love interests, their romantic triangle occupying much of the series. Official Gainax art consistently supports this notion.

This first post will focus solely on Pen Pen’s relationship with Shinji, as his relationship with Misato is quite complex enough to warrant another post. I've decided to begin the topic of Pen Pen’s sexuality with Shinji, as it is an arc that last the entire run of the show.
As you know, Pen Pen is first introduced in episode 2. His very first appearance sets up his multifaceted relationship with Shinji as well as the budding love triangle between Pen Pen, Shinji, and Misato. Although Pen Pen is already in a committed domestic partnership with Misato, he is instantly drawn to the sultry young boy. It would not be too much of a stretch to say that Pen Pen desires Misato emotionally and Shinji sexually.

Pen Pen’s initial interactions with Shinji could easily be described as tsundere, following the typical romantic comedy formula of mutual hostility giving way to attraction, as Shinji’s horrified reaction to seeing Pen Pen in the bath and his constant bickering with him in the manga clearly show.

Pen Pen and Shinji’s mutual attraction is shown very explicitly in episode 10, in a way that must have shocked the original audience. No doubt the shows’ creators would have gone much further had it not been for network restrictions. While many have speculated that Shinji’s erection is caused by hearing Misato and Asuka tickle each other nearby, I regard this as mere fanwanking. The immediate cause of Shinji’s erection is clearly Pen Pen, as he is standing directly in front of Shinji. Notice that Shinji does not blush until Pen Pen stares at his tumescent member.

Over time, the two draw closer. Pen Pen no longer antagonizes Shinji, and Shinji is no longer impatient with Pen Pen. In episode 7, they are already shown dining together, as if they were old friends---or a married couple. In episode 9, they are shown acting in unison as they wait for Asuka to emerge from the WC. Their souls have achieved oneness, you might say.


The manga shows even more clearly than the anime that their bond has become one of trust and affection, as this page demonstrates. Pen Pen is depticted staring at Shinji with hearts in his eyes as the boy gives him his meal; he has replaced Misato as the provider of food, food of course being a metaphor for love. Rather ominously, however, Shinji’s expression appears to be morose and apathetic.

Episode 15 marks the turning point in Shinji and Pen Pen’s relationship. Shinji, unsure of his sexuality and unable to ignore conventional mores in pursuit of a relationship with a male bird, acquiesces when Asuka, his human roommate, offers to kiss him. Pen Pen watches their foreplay in crestfallen silence and subsequently retreats into his room, heartbroken. When he closes the door of his refrigerator, he no doubt begins to sob.

In episode 23, we see just how far Pen Pen’s affection for Shinji extends. Despite his formerly warm relationship with Misato, he is unwilling to allow Misato to hold him, uninterested in anyone but his inamorato, Shinji.

Pen Pen’s relationship with Shinji is subtly explored in both the TV and movie endings. In episode 26, Pen Pen is shown as a mere bobble-headed doll on Shinji’s desk, signifying that he has become an object for the boy’s gratification, his own feelings ignored. In the final scene of the original series, Pen Pen, the bird who loved Shinji without any hope of reciprocation, is shown greeting him at the end of his journey, all animosity forgotten.

EoE explores Shinji and Pen Pen’s relationship in a darker, more complex fashion. In one of the film’s most memorable scenes, Pen Pen re-imagines the night in which Shinji broke his heart by betraying him with Asuka in episode 15. Instead of humiliating Pen Pen with a kiss, however, Shinji takes things one step further and confesses his feelings to the girl. Horrified that Shinji has chosen Asuka over him, Pen Pen can only watch in shock, before secretly rejoicing in the brutal murder of his love-rival.

The keepsake photo is Pen Pen’s final appearance in the series, and it is a very significant one indeed. Pen Pen is held by Hikari at arm’s length from Shinji, never able to touch the one he loves. Note Pen Pen’s tired eyes and world-weary expression. This is the end of his relationship with Shinji.
