We learn that the name of Harris' organization Section 31, although never officially revealed in this or the previous episode, is derived from Article 14, Section 31 of the original Starfleet Charter, which makes allowances for "bending the rules during times of extraordinary threat". It is the only direct reference - and, thus, confirmation - in this two-parter of Section 31, a secretive organization first introduced in Inquisition (1998).
This episode and the preceding one (Affliction (2005)) were written to explain the makeup change in Klingons between Star Trek (1966) and Star Trek: The Motion Picture (1979), which had been acknowledged as canon in Trials and Tribble-ations (1996). Phlox also mentions "minor neural re-ordering" as a side effect, which would explain the behavioral differences between the more subdued (and sometimes even cowardly) Klingons from TOS and the more feral and fearless Klingons from other series. The writers of Star Trek: Enterprise (2001) hoped their take would find a way of explaining the change, while simultaneously telling an interesting story.
The process of transferring a crewman between starships with a tethered line is based on the wet-navy practice of using a bosun's chair to transfer a high-ranking officer from one ship to another through a line tied to the ship's mast.
The graphic designers mistakenly added the USS prefix to both the Enterprise and Columbia in episode artwork. Neither of the ships were ever designated USS.
Krell was a brand of toothpaste named in a Monty Python sketch.