Art Evolution: The design of Daedalus, which differs significantly from the schematics glimpsed over on SG-1 the previous year. The initial design was closer to the Prometheus whereas the final design here has significantly evolved away from the X-303's template.
Weir: [calmly walks up then hugs him] Yes... yes, you are...
Batman Gambit: As Weir points out during the war council, the central flaw of the 'Fake the Destruction of Atlantis' plan is that the Wraith know the Expedition has access to the Ancients' cloaking technology. So, there's a good chance they'll quickly realize what's going on once the Expedition implements the ruse. Teyla's solution is to connect to the Wraith Hive Network and feed them false impressions of impending destruction. Convinced the Expedition is going to destroy the city, the Wraith will break off their attack rather than aid their enemies (which will give the Expedition the breathing room to switch over to the cloak). It works (though not without complications from Ford's escape).
The Bus Came Back: Dr Novak, the hiccuping scientist last seen aboard Prometheus returns here, sans hiccups.
Cool Ship: The Daedalus, which makes it formal debut here after the setup in SG-1's "Moebius, Part 1" the previous year.
Continuity Nod: After the Wraith dispatch reinforcements, Rodney points out to an incredulous Caldwell that the Expedition has previously confirmed the Wraith have access to at least 60 Hive Ships (not counting Darts, Cruisers, or other support craft).
"Eureka!" Moment: When the Expedition realizes they can't win the Siege, Zelenka grimly remarks that as long as the Wraith know they're there, they'll just keep coming (as Atlantis is their only way to get to Earth). This gives Sheppard an epiphany: They don't have to beat the Wraith. They just have to trick them into thinking Atlantis was destroyed by their bombardment.
Failed a Spot Check: Downplayed, but apparently nobody aboard the Wraith Hives thought to dial the Atlantis Gate after the city was "destroyed" just to make sure it really was gone (either now or throughout the rest of the Season).
Foreshadowing: The Wraith Cruiser that descends and draws parallel to the Daedalus during the second space battle. Sheppard thinks they're trying to board the BC-304, but what they were actually up to will be revealed next episode.
Gunship Rescue: Daedalus begins a career of these here, making short work of a hive ship and sending the cruisers fleeing into hyperspace.
Mercy Kill: Discussed in-story. After having been partially fed upon by a Wraith in the Teaser, Everett finally understands what Sumner went through during "Rising" — and that Sheppard was completely justified doing a mercy kill. Everett forgives Sheppard for killing Sumner and wishes the Major had been there for him too.
Nothing Is the Same Anymore: Atlantis now has a ZPM and can finally utilize systems they were unable to power during Season One (such as the Shield Generators). They also have finally re-established contact with Earth and now have a supply line and access to the SGC's spacecraft like the F-302s and new BC-304s. While the Wraith believe Atlantis has been destroyed, the Expedition now has to be very careful, as any Expedition personnel sighted or captured on Pegasus worlds will shatter the charade. Finally, Ford has gone renegade and the Expedition's flagship team has lost one of its original members.
Screw This, I'm Out of Here!: The Wraith Cruisers after the final Hive's destroyed. Subverted, though, in that they were jumping away to signal reinforcements.
Spanner in the Works: The 'Fake the Destruction of Atlantis' plan is nearly single-handedly derailed by the now-insane Ford. He steals a Puddle Jumper and activates the Gate...just as Rodney's switched off the shield and activated the cloak. It's sheer luck that the Wraith's sensors don't detect the Gate activity through the nuclear fallout.
There Is No Kill Like Overkill: The Wraith reinforcements. Again, the Expedition knows from "Underground" last Season that the Wraith possess access to at least 60 Hive Ships (and again, not counting Darts, Cruisers, or other support craft) The flotilla inbound to Lantean thus constitutes 20% of their entire main fleet. Considering the size of the Wraith's domain and redistributing those fleet assets will impact ongoing cullings, it speaks volumes about how badly the Wraith want access to Atlantis and from there to Earth.
Uncertain Doom: Colonel Everett after being partially fed upon by a Wraith. While he's shipped out with the other casualties, his ultimate fate is never revealed. The closest we ever get to an answer is Season Three's "Common Ground", where Becket grimly reveals that a large percentage of those who survive a partial feeding die anyway from complications as a result of strain on the body systems. Everett's not explicitly stated, but it's possible Beckett was alluding to him.
What You Are in the Dark: When his bodyguards are felled by Wraith soldiers, Rodney stands up to them with only a pistol.
