This three-part story arc established that in the 22nd century, genetic engineering was completely banned on Earth after the Eugenics Wars, even for genetic research which could be used to cure critical illnesses. At the end of the story, Archer expresses his hope to Dr. Soong that research into genetic engineering that could cure life-threatening diseases would actually be resumed. According to Dr. Bashir in Doctor Bashir, I Presume (1997), by the 24th century genetic engineering was indeed used by that time to treat serious medical conditions, though trying to genetically engineer Humans with "superior" abilities was still banned.
After Dr. Soong and the Augments escape from Cold Station 12, they take the Klingon Bird of Prey into a region of space with radiation from supernova remnants, which the Klingons called Klach D'kel Brakt and Soong nicknames "The Briar Patch." This is the same region of space containing the Ba'ku homeword in Star Trek: Insurrection (1998). This region is also the site of the Battle of Klach D'kel Brakt, where Dahar Master Kor led the Klingons in a glorious victory over the Romulans in 2271, and nearly a century later, would re-create that battle on one of the holosuites in Blood Oath (1994).
The name Noonien, in the Star Trek universe, is shared by Khan Noonien Singh and Noonien Soong, Data's creator. Although the connection is not made explicit, this trilogy establishes a possible connection between the two characters, suggesting that a later member of the Soong line may have decided to name his son Noonien in honor of Khan, the most famous of the augments.
Dr. Arik Soong (Brent Spiner) mentions that artificial intelligence may best serve humanity. Arik Soong is the ancestor of Dr. Noonien Soong from Star Trek: The Next Generation (1987), who came to invent the android Data.
At the end of this episode, Arik Soong claims "I've been thinking, perfecting Humanity may not be possible. Cybernetics. Artificial lifeforms. I doubt I'll finish the work myself; might take a generation or two." This is a direct link to the Soong family's work in upcoming centuries, which see the creation of the androids B-4, Lore, Data, and Juliana Tainer by his great-grandson Noonian Soong.