The object that Archer uses to fatally stab a Reptilian soldier is a miniature replica of the Zefram Cochrane statue described by Geordi La Forge in Star Trek: First Contact (1996).
According to the writer Mike Sussman, this story was originally pitched as an episode for Star Trek: Voyager (1995) with Kathryn Janeway as the afflicted captain and Chakotay as her caretaker.
The battle scene establishes that the Enterprise had received tactical advancements from Shran, who later plays an invaluable role in preventing the events of this episode from ever taking place in Proving Ground (2004) and Zero Hour (2004).
An Earth convoy destroyed in the Mutara system is mentioned by Soval, a reference to the site of a battle between Kirk and Khan, also depicted in Star Trek II: The Wrath of Khan (1982).
T'Pol tells the amnesiac Archer that they are on "the fifth planet of the Ceti Alpha system." This is Ceti Alpha V, the same planet to which Captain Kirk exiled Khan Noonien Singh and his crew in Space Seed (1967). In that episode, Ceti Alpha V was described as "habitable, although a bit savage, somewhat inhospitable". 'Twilight' takes place 111 years before 'Space Seed', with Trip describing the planet as "barely Minshara-class". Although the landscape seen through Archer's windows seems to be quite pleasant, the script for 'Twilight' describes Ceti Alpha V as a "dry, inhospitable-looking class-M planet", with human settlements located in one of the "few occasional patches of vegetation", thus fairly consistent with the description in 'Space Seed'. However, in Star Trek II: The Wrath of Khan (1982) (which takes place 15 years after 'Space Seed'), Khan states that Ceti Alpha V was turned into a wasteland by the explosion of Ceti Alpha VI, which altered the orbit of Ceti Alpha V. According to Wrath of Khan producer Harve Bennett, the idea was that the Ceti Alpha planets had varying and unstable orbits, which somehow caused planet VI to explode. This shifted planet V farther from the sun and turned it from the "harsh but survivable" world seen and described in 'Twilight' and 'Space Seed' into the wasteland seen and described in 'Wrath of Khan'.