The game makes several direct shout outs to well-known science fiction novels, films, and pop culture.
- Juro is a huge fan of the kaiju film Deimos, a 1954 classic which spawned a massive franchise in the years since its release. He also has an appreciation for Exterminator 2.
- Natsuno if a big fan of E.X.T., UFO Wars, and The War of the Worlds. E.T., in particular, serves as an inspiration for her route.
- Megumi ends up making a "contract" with a mysterious cat that promises to grant her wish in return for "shooting witches". Later on, the same cat jokes about a time machine in a desk drawer and having a fourth-dimensional pocket.
- When you select Miura's unit during fights, he says that he's "not throwing away [his] shot."
- The High Quad Kaiju are an Expy to the alien Tripods from The War of the Worlds, with the game even dropping a quote from the book when they first show up.
- Takamiya's story setup (a sukeban is arrested and put to doing her own investigations) is a dead ringer for Sukeban Deka, with even the uniform of the two being similar, and Yuki's name being only a few letters off to sound like Saki Asamiya. Her first name may also be a shoutout to the Saki Asamiya's actress: Yuki Saito.
- In 2188, Megumi's father pleads to Takatoshi to open the colony airlock and let his daughter inside. Takatoshi replies "I'm afraid I can't do that."
- "Groundhog Day" Loop in Nenji's route is a homage to the film Source Code. As is, partly, the "computer simulation" concept of the setting.
- The setting and plot owes very much to Megazone 23. (Even the recreation of different time periods in different "cities" was described in Megazone 23 background pamphlets.)
- Miyuki Inaba's design and role in stage 2-10 feels like an homage to Super Dimension Fortress Macross (in addition to being an obvious homage to Eve from Megazone 23).
- The Reveal at the very end of the game that the 13 protagonists plus Tamao and Okino are the only remaining actual humans and were incubated in pods until ready for emergence is reminiscent of The Matrix.
- The overall format of the game, in which you switch between multiple different homages to different genres assigned to different characters over the course of the game, alongside switching between characters on a wheel styled character select, is a subtle but clever homage to Live A Live.
- The title, basic premise of semi-realistic Super Robot vs. Kaiju, the notion of the Mechs potentially damaging the pilots' nervous system and different generations of them that emphasized different weapons and tactics all harken back to Pacific Rim. The Gen 2 Sentinels in particular look very similar to Cherno Alpha without the giant cooling tower on top.
- Detective Onishi, with his shabby brown coat, gravelly voice, and squinty expression, is a dead ringer for Columbo.
- Perhaps unintentionally, but to Nick Sagan's Idlewild, which most of the plot of 13 Sentinels mirrors.
