It was nice of Archer to tell Soong that Enterprise was going to initiate the station's self destruct sequence. It gave the Augments that extra few vital seconds to shut the thing down and foil his plan. Always good to see somebody show such consideration to their enemies that way.
At some point, Phlox spent a few months working at Cold Station 12.
A 47! When Soong tries to get into Cold Station 12, the screen comes up with "Initiate Protocol 047".
This is the first episode in which we see Dr. Lucas, who has several times been mentioned as Phlox's pen pal.
The diseases listed on Malik's screen as being stored on CS-12 have all been referenced in previous Trek episodes :
Xenopolycythemia - McCoy had this in TOS : "For the World is Hollow and I Have Touched the Sky"
Synthococcus Novae Type A - Sevrin had this in TOS : "The Way to Eden"
Rigelian Fever - Flint had this in TOS : "Requiem for Methuselah"
Rigelian fever (gram positive) - presumably some sort of variant of the standard disease which Flint had
Tellurian Plague - mentioned in TNG: "A Matter of Time"
Anchilles Fever - the Enterprise-D was seeking a vaccine for this dreaded disease in TNG : "Code of Honor"
Andronesian Encephalitis - an Enterprise-D crewmember had this in TNG : "The Dauphin"
Archer's father died when he was 12.
The BoP has a small hangar between its nacelles.
I would like to have seen the issue of Earth's reaction to the Augments gone into a little more deeply. For instance, Archer tells Smike that the Augments are not going to be punished by being put in jail. Okay... but what would happen to them? Assume that Archer was able to capture them all alive. Presumably the Augments on the Bird of Prey would be handed over to the Klingons for the murder of the Bird of Prey crew, which is a death sentence in itself given the Klingon justice system. But even if they stayed on Earth... would they really have just been freed to mix in with the general population? It's hard to imagine that that would be allowed, but on the other hand just how severe are Earth's laws against genetic engineering? We know from Bashir and others that even two hundred plus years after this, augments can't serve in Starfleet, and that even minor character 'defects' like promiscuity are enough to get an augment locked up forever. Would Earth lock people up just for being augmented, let them roam free, or come up with a half-way solution like some form of monitored probation? I'd like to have seen the episode go into ideas like this a little more.
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