No, you aren't dense at all.

Part one, the past, the narrator/observer is John's old friend Dex, who along with Mitch was killed in action. We meet them in the first season episode Home.

Part two, the present, the narrator/observer is Atlantis herself.

Part 3, the future, is told from the perspective of the child John and Rodney may someday have (the details of which I've left ambiguous.)

I'm glad you liked it:)