The episode was written and storyboarded by Adam Muto and Rebecca Sugar, from a story by Mark Banker, Kent Osborne, Patrick McHale, and series creator Pendleton Ward.

In this episode, Finn, Jake, Princess Bubblegum, and Marceline the Vampire Queen form a band in order to defeat the Door Lord and recover what the creature had stolen from them.

When they realise she only wanted to spend time with the friends, Marceline feels embarrassed and chases Finn, Jake, BMO and Bubblegum from the Door Lord's abode.

"What Was Missing" was written and storyboarded by Rebecca Sugar and Adam Muto from a story developed by Mark Banker, Patrick McHale, Osborne, and series creator Pendleton Ward.

"[5] She later likened the theme of the episode to a quote by Bob Fosse—“The time to sing is when your emotional level is too high to just speak anymore"—noting that she "really wanted to try for that feeling.

"[5] When looking over the episode’s plot prior to it being storyboarding, Sugar noticed that the interactions between Marceline and Princess Bubblegum recalled the animosity shared between two exes.

The production crew of the series approved of this story approach, but due to restrictions at Cartoon Network, the writers were unable to explicitly confirm this information in the episode.

[6] All of the songs featured in the episode were initially composed by Sugar, who released her demo version of "I'm Just Your Problem" on her official Tumblr page.

[13] Dana Piccoli of AfterEllen.com enjoyed the way the episode "alluded to perhaps, more than platonic feelings between" Princess Bubblegum and Marceline, as well as the fact that "What Was Missing" was underlined by potential lesbian "subtext".

Club named the episode one of the ten additional installments of the series that illustrates that "emotional complexity" lies "beneath Adventure Time's weirdness".

[16][17] The controversy largely began after an accompanying "Mathematical" recap—a behind the scenes video series produced by Frederator Studios, one of the show's production companies, that implied that there were lesbian relations between Princess Bubblegum and Marceline and that the writing staff actively seeks input from fans.

[16] Ward later addressed the issue and gave a more neutral view, saying that, because there were "so many extreme positions taken on it all over the Internet", he did not "really want to comment on it [because] it was a big hullaballoo.

"[20] In August 2014, Marceline's voice actress Olivia Olson told a crowd of fans gathered at a Barnes & Noble book signing from The Adventure Time Encyclopedia, that, according to Ward, Marceline and Princess Bubblegum had dated in the past, but that because the series airs in areas that discourage homosexual relationships, the show has not been able to officially clarify the relationship in the series itself.