Not Just Friends by AndromedaMarine
The First Tragedies
One year passed and Peter Grodin died. Two years passed and who-knows how many soldiers died during the siege. Three years passed and Carson Beckett died. Four years passed and Elizabeth Sheppard died, leaving her husband to care for their two daughters. John still had Rodney, Teyla and Ronon as his team; Lorne somehow managed to strike up a relationship with Laura Cadman and now they were engaged. Rodney and Jennifer Keller were getting closer each day and the two off-worlders had been together for a long time.
Realizing that Atlantis was an actual city and not just an expedition anymore General Hank Landry revised regulations allowing marriages and children. His first clue was the birth of twins Antissa and Nara Sheppard. His second clue was the birth of Torren John Emmagan not long after the Sheppard kids were born. Antissa and Nara were five months when their mother died. It tore John apart to lose his leader – even more so to lose his wife and mother of his children. From that day forward he was more careful than usual on missions – he made sure that every time he went through the gate he'd be coming back.
Things just weren't the same with Sam Carter as their leader – she didn't have the same diplomatic skills that Elizabeth had possessed, although her experience with the Stargate outranked everyone, even Rodney. John knew that one day, quite soon, he would have to choose another Atlantean couple as his children's godparents. In reality if he died Antissa and Nara would be under the protection of the city, but everyone needed parents.
When Rodney and Jennifer married John had his answer. The newlyweds had given the Colonel a heartfelt 'yes' and decided to spend their honeymoon on New Athos. They were gone for one week when they got word that Radek had been seriously injured while working on an Ancient device. Rodney insisted that they return at once – to give moral support and so he could figure out what went wrong with the device.
Jennifer tended to Radek, who had massive burns on over half his body. It was a miracle he lived, she had said. Rodney told Radek to be more careful, and began to watch out for John on missions. It was now nearing the end of their fifth year on Atlantis and Rodney was dreading the day when someone he knew, cared about and loved died. It had become a pattern that was heart-wrenching and painful every year when the inevitable approached. Neither John nor Rodney could keep their emotions in check for long. It could be either one – John or Rodney, maybe Evan, or even Chuck Campbell. Perhaps this time it would be Jennifer, or Katie. God forbid Sam die, leaving their city once again leaderless. Or maybe Radek. Ronon, or Teyla? John couldn't stand it.
The first tragedies they all dealt with, the group of mourners at the time including Carson and Elizabeth, informed and reminded every member of the expedition that their presence there did not come without inevitable losses and unending casualties. The first tragedy for Antissa and Nara was the death of their mother. Their second tragedy was approaching.