If you are constructing a ringworld, another empire might contact you out of concern that you are using it to create a devastating weapon. This is a reference to the Halo series, in which the Halo worlds were actually weapons to wipe out life.
The event “The Gun Pointed at the Head of the Universe” shares the same name as a song from the first Halo’s soundtrack.
The War in Heaven event is a reference to the Second Shadow War in Babylon 5. It also can result in the trophy/achievement “Last, Best Hope,” which is a reference to a quote repeatedly said in Babylon 5.
The name “War in Heaven” may also refer to the Book of Revelation.
The endgame crisis events all resemble similar events from popular science fiction series.
The Prethoryn Scourge – either the Tyranids from Warhammer 40k or the Yuuzhan Vong from the old Star Wars Expanded Universe novels
Extradimensional Invaders – the Devidians from Star Trek: The Next Generation
The Contingency – the Reapers from Mass Effect
The Sanctuary system’s ringworld is a reference to the Ringworld novel.
Pre-release streams led to the invention of “the Blorg Commonality,” an empire of ugly-yet-friendly aliens who just want to make friends. Fans liked the idea of the Blorg so much that they were included in the game, along with the “Fanatic Befrienders” personality trait for empires with the ethics and traits of the Blorg.
Their name, “the Blorg Commonality” is also a play on the Borg Collective from Star Trek, an alien race that seeks to assimilate other races.
The Honeymooners anomaly event leads to the discovery of a travel guide called the Hitchhiker’s Guide to the Galaxy, which is of course a reference to the book series The Hitchhiker’s Guide to the Galaxy.
The species Prikki-Ti is also a reference to the Krikkit species in the book.
The notification “Crystalline Entities are Unbreakable” while researching Crystalline Entities is a reference to the fourth part of JoJo’s Bizarre Adventure, Diamond is Unbreakable.