SG Atlantis Q: "McKay & Mrs. Miller" & "Phantoms"

[God Magnus]

I recently started catching up on SGA (ah, Netflix, how I love thee) and I've gotten to season three. I watched "McKay & Mrs. Miller" and at the end of the ep, I was under the impression that the ZPM was drained completely and they were essentially running on back up power. Then in the next ep "Phantoms" everything seems back to normal, bright lights, Stargate function and all. Did I miss something? I thought they didn't have back up ZPM's or at this point in the story did they only have a few spares? Or is this touched on later in the season?

I know it's a small nit pick but it's been bugging me since I saw these eps back to back. Thanks for any fino.

 

[David cgc]

They're running on the Naquada generators, again, like in season one. They can't, say, put up the shield or cloak the city anymore.

 

[Brent]

They can dial local gates with the Naquada generators, but not Earth.

 

[God Magnus]

Ah gotcha. Thx.