Captain Archer makes a major referance to Captain Picard and the Enterprise E Crew when he mentions the events of Star Trek VIII First Contact referring Picard's crew as a group of humans from the future. Also The Borg are referred to as a group of Cybernetic Creatures from the future.

There is a very major reference to Star Trek VIII First Contact as the date given in the episode "In A Mirror, Darkly, Part 1" mention the date April 5th 2063. This is 2 days after Picard and the crew of the USS Enterprise E arrive in Dr. Cochrane's era to stop the Borg from destroying the Phoenix and disrupting First Contact.

This episode screws up YEARS of hard work by the writers of TNG & even some of the writing on Voyager. Q flung the Enterprise-D in the path of a Borg cube in TNG's season 2 episode, "Q-Who?", the events of which are referenced by Janeway in "Scorpion, Part I". This encounter between Picard and the Borg cube is what sparked the Borg's interest in humanity. Is this episode suggesting that the message sent in Archer's time was not received by the Borg, or that part of it was, and it wasn't until Picard met the cube in the 24th century that the Borg realized about whom the message was speaking, or what? Throw out excellent trek episodes like "Best of Both Worlds, Part I" and "Best of Both Worlds, Part II", "Emissary", "Scorpion, Part I" and "Scorpion, Part II", and the movie "First Contact", because "Regeneration" just messes 'em all up.

The "cybernetic creatures" are of course the Borg, who have made numerous appearances over the years since their introduction in the second season TNG episode, "Q Who?". The two Borg found in the arctic are survivors of the sphere that was destroyed by the Enterprise-E in the eighth movie, First Contact.

Phlox tells Reed that he once encountered a species named the Bynars. The Bynars appeared in The Next Generation episode "11001001". This is the first episode that they have been mentioned since "11001001".