Back on Earth the leaders of the alliance worlds are filled in on the situation with the unknown ship and they request all ships look out for it and report immediately if it's encountered, Col Swanson returns to the Alliance.
After the debrief O'Neill and Carter join Daniel Jackson in his office to discuss the message "Hey Sam I heard you had a situation out there" says Daniel "Yes it was pretty tense for a while, any look figuring out what the message means?" asks Carter and Daniel explains that the language used in the message is one the Ancients used when they first arrived in our galaxy millions of years ago and it's not clear why but they stopped using it shortly after their arrival and that's why he didn't recognize it at first, and the only reference he has to it is from photos taken of a stone column in the ruins of the Ancient lost city.
"Are you saying the message came from the Ancients?, the ship we encountered didn't look Ancient to me." asks Carter and Daniel says he really doesn't know and that he's sent the message to McKay to run through the Atlantis database and see if he comes up with anything.
"Well let's hope so. Sir any progress on the device we found?" asks Carter to which O'Neill replies "Nothing yet but after what just happened I'd rather have you working on it. I'll arrange transport for you to the facility." and Carter heads off to continue running tests on the mysterious device.
Back on P3R-272 the figures in black are standing at an Ancient console pushing switches and on the display in front of them are letters in the same language as the message the Alliance received and the letters are moving around as they push switches as if trying to get the right sequence.
The cylinder they brought with them is wired in to the side of the console like some type of power source and beneath the console is a translucent window with a blue crystal locked away behind it. Eventually they manage to enter the correct sequence and the window opens allowing them to reach in and grab the crystal, they lift it up and step away from the console then at that moment they are transported out of the room on to the unknown ship which is now in orbit above the planet and it flies away.
At the same time as the crystal is taken from the Ancient console on P3R-272, in Pegasus on Atlantis McKay is running the message Daniel sent him through the Ancient database and arguing with Zelenka over how best to fit the Jumpers with hyper drives.
McKay turns to his laptop and begins entering some code "Look the math is perfect this is the most efficient way to do it" shouts McKay "No, no your power calculations are all wrong" replies Zelenka "Oh really" says McKay "Yes really" replies Zelenka "The calculations are fine you don't know what you're talking about, I'm right you're wrong.." at this point Woolsey walks over and tells them to keep it down and work together instead of shouting at each other.
"He started it" says McKay to which Woolsey replies "I don't care who started it just stop it..people are trying to work in here and you're acting like school children".
Zelenka gets on the laptop "Let me show you" as Woolsey turns to walk away and they start arguing again but suddenly the city's alarms go off and every screen displays a flashing red symbol "Now what did you do" shouts McKay "I did nothing, it wasn't me" replies Zelenka.
Sheppard, Ronan and Teyla run into the control room to find out what's going on just as Atlantis is locking down and closing doors behind them "What the hell's going on Rodney" asks Sheppard "I..I..I ….get out of the way" replies McKay while pushing Zelenka out of the way and getting back on his laptop "I'm locked out, I don't have access to anything" says McKay.
The shields activate and Atlantis' drives start up and begins taking off "MCKAY!" shouts Sheppard "I can't do anything!" shouts McKay "It's doing it by itself" Sheppard, McKay and Woolsey look at each other in disbelief "There's nothing I can do" says McKay, Sheppard isn't too happy about what's happening "We have teams off world Rodney, you need to stop the city taking off" "I can't!" replies McKay.
Woolsey looks at a display and asks what does the symbol mean "Are we under attack, is it a viral outbreak" McKay replies "No if it was it wouldn't have locked us out we would still have limited access to some systems but we're completely locked out."
Woolsey asks "OK what were you doing before this happened?" McKay looks at the laptop "We were working on a way to fit Jumpers with hyper drives and running a database scan on a message sent from Dr Jackson" Woolsey "Could the message have affected the system in some way, maybe it's a virus" to which McKay replies "No. The database is isolated from the main systems it has no direct access and can't affect them even if it was a virus. I scanned it before running it...I'm not an idiot" McKay looks over to Zelenka while saying the last part of the sentence.