Carl Binder penned Ghost in the Machine which first debuted on 15 August, 2008.

Sheppard (Joe Flanigan) and his team are returning from a mission (flying monkeys ) when something happens to their puddle-jumper as they attempt to pass through the gate. Tumbling away into space, they find out what happened.

Something is affecting their ship, after the power is restored, somehow, they are able to get home. So what happened? A group of beings are stuck in sub-space. They moved from the puddle-jumper to Atlantis, and find ways to communicate, once they get around the power outages and shortages. They want help to return to real space, but the things they say and claim seem odd and suspicious.

Can they be trusted? Because one of the claims the being makes is that one of the beings is Elizabeth Weir (Torri Higginson, or in this case Michelle Morgan, who played Weir in her first appearances).

The story ties into the Replicator mythology and serves to wrap up Weir’s and the Replicator stories.

Weir is a Replicator and she and some of her allies are still trying to Ascend. They uploaded their essence into subspace, eschewing their physical bodies, in a hope to reach Ascension quicker.

But things aren’t going to be that easy. Weir creates a Replicator body, just in time, because there are other Replicators on the way – and they want bodies too. Can an agreement be reached? Can they all be trusted? What is their endgame?

In the end, Weir makes a decision that closes her story, and is the last time we hear about the Replicators (though there is a new series coming so… who knows?).

The Shrine was written by Brad Wright and first aired on 22 August, 2008.

McKay (David Hewlett) is infected with a disease known in the Pegasus Galaxy as second childhood. It slowly infects his mind, taking away abilities and knowledge, including memories.

Keller (Jewel Staite) is trying to figure out how to help him, and they even bring Jeannie (Kate Hewlett) to Atlantis to say goodbye.

We get a flashback to how things happen, and see something we’ve never seen before, Sheppard and his team, atop a stargate, because the land has been flooded by a glacial dam breaking. And whatever was in it has had an effect on McKay.

Ronon (Jason Momoa) knows of a place, a shrine, that may help, but it’s dangerous. He’ll try it if Jeannie will. It offers one last day as who they are, before they pass. Ronon, Teyla (Rachel Luttrell) and Jeannie argue for the mission, Woolsey (Robert Picardo) finally agrees.

Will they be able to find a cure at the shrine, or will they have to say goodbye?

Watching the Hewletts together as they confront the possibility of loss and saying goodbye is really powerful stuff. I love when they are onscreen together.

It’s a powerful and emotional episode. I really like this one. It’s smart, well-written and the entire cast are on their game.