Transcripts for the show are available at a few sites.
Heads-up for Wraith fans. Look out for:
1) Content warning: misgendering and also non-canon pronouns on some sites. Some transcripts refer to male Wraith as the objectifying pronoun “it,” even though the actor credits state male roles and Wraith themselves use male pronouns to refer to one another, with and without human presence.
2)Content warning: editorializing. Some sites sprinkle the dialogue with writer opinion, often negative and not canon. Only the dialogue is canon.
2) Incorrect info: Kenny. Some old transcripts incorrectly refer to Todd’s underling in “Enemy at the Gate” as Kenny, even though this officer had different coloration, facial markings, and beard length. This misnaming violates sources 1-3 in the source hierarchy. Many fans call the EATG officer Jareth.
In spite of some errors, they are still good resources.
GateWorld’s is most recommended, as there is no Kenny error and speaker names are noted. As of 5/2018, there is still misgendering and editorializing though.
*GateWorld. Misgendering but no Kenny error. https://www.gateworld.net/atlantis/
*Springfield. Lines only, no Kenny error or misgendering, but also no speaker names: https://www.springfieldspringfield.co.uk/episode_scripts.php?tv-show=stargate-atlantis
*Stargate Solutions. Misgendering and Kenny error. http://stargate-sg1-solutions.com/wiki/Transcripts#Stargate_Atlantis
*Scifi Media. Misgendering and Kenny error. https://scifi.media/stargate/transcripts/#atlantis
Wikia. Misgendering and Kenny error. http://stargate.wikia.com/wiki/Category:Atlantis_episode_transcripts