Basically, it's a bunch of what are called SpaceGates in SGA, Gates floating in Space, which were dropped in place at various intervals between the Pegasus Galaxy and the Milky way, in the middle the last gate from Pegasus faces the first gate from the Milky Way, and that can be used as a buffer zone. Enough of that, though... I don't wanna end up sounding like David Hewlett.
But while Mackay is showing off he and Carter's innovation, he detects an odd sensor blip, which turns out to be an Atlantean ship traveling to Earth at 0.99999 times the speed of light, making it a bear to catch up with!
The captain of this ship is "Helia" (Megan Leitch aka Samantha Mulder), and if she is a common Atlantean, it explains why the race of Ancients who were technologically superior were defeated - They were also stupid! Basically, Helia takes over Atlantis, kicking out all of those who had been running the place and protecting it for them and allowing only two people to stay: Richard Woolsey (Robert "The Doctor" Picardo) and one Jack O'Neill (two l's).
These Atlanteans make assumptions about the state of the universe that maybe were correct 10,000 years ago, but are just not true now. And they pay for it when Replicators invade. Fortunately, Jack O'Neill and Woolsey have the sense to run and hide, while Helia used her last breath to protect them, to her final credit.
But John Sheppard is on Earth, trapped while Tayla and Ronon are on some butt-planet in the Pegasus Galaxy being wooed by the new leader of The Genii.
So the conundrum is how to get the main Stargate Atlantis team (and Weir) back to Atlantis - Without SGC's permission or help. But that solution was in my first paragraph, or, "How to Hijack a Bridge".
And of course, Rodney has an idea on how to deal with Replicators, unless it all goes sideways as usual. But it was great to see Richard Dean Anderson bounce off Robert Picardo, two great actors amusing us and themselves. Of course there are goofs and scientific inaccuracies, but that's TV for ya- It does not deter from a great set of "sweeps week" episodes.