When Atlantis returns from Earth to the Pegasus galaxy, the city is ready for war.
In the past, the SGC staffed and equipped the expedition as, essentially, glorified security guards for Atlantis, its secrets and its stargate. John never had any illusions that if the SGC wanted the Atlantis expedition to do much more than hold the line, they probably would have chosen anyone but John Sheppard as military commander.
After Kenny's attack on Earth, the SGC is serious: John can tell, because he's not in charge anymore. Sure, he's still military commander of Atlantis, but now there's a Brigadier General overseeing military operations in the Pegasus Theater, directing the Daedalus and the Hammond and a fleet of F-302s in a series of tactical strikes against the Wraith, with Atlantis acting as their base of operations.
Peace is a daily, a weekly, a monthly process, gradually changing opinions, slowly eroding old barriers, quietly building new structures. Rodney finds that relationships are a lot like that, too.
John is sitting out in front of Ronon's, sprawled out all over a chair like he just sort of melted onto it, engrossed in- and bending the absolute hell out of, as usual- a paperback. As Rodney starts to make his way over, John spots him and gives him a wave, probably in response to Rodney's tripping over a table leg and almost eating patio.
Life can break your bones. It can also stitch you back together.
Rodney winced.
And – yes - that was the one he'd been waiting for: alarm number three, located approximately three feet from his head, pitched precisely to make his brain explode. He fumbled with the crystal in his hand, almost dropping it in his haste to shove it back into the console, swearing viciously and abruptly audibly as the alarm finally cut off.
"Rodney?"
When Rodney gets to the armory, he has to step aside as four determined marines in full gear get out and almost trample him, walking briskly towards the gate room. Glancing inside, Rodney notes that it leaves only John in the room: perfect. There's no going back, then, so Rodney takes a big breath and he's talking even before he crosses the door's threshold. Here goes nothing.