“First Strike” is the twentieth episode of season three of Stargate: Atlantis and the season finale.
The Asurans, the human-form Replicators from the Pegasus galaxy who were encountered in episode five, “Progeny”, and episodes ten and eleven, “The Return Part 1” and “The Return Part 2”, of season three, are apparently building warships. Given that they know the location of Earth, this is worrying.
The new Earth ship the Apollo, using a weapon called Horizon, is used to launch a pre-emptive first strike on the Asuran homeworld and destroy the ships.
The Asurans in their turn launch an attack on Atlantis, damaging the Apollo in the process, using an energy beam directed against the city’s shield.
With the power to the shield going to fail eventually, the decision is made to submerge the city, as was done by the Atlanteans when they were attacked by the Wraith.
A cliffhanger ending to the episode, with the story continuing in season four‘s “Adrift”. Hopefully, they haven’t just killed off another major character, but I’m not holding my breath.