Important episodes in Stargate Atlantis?

Okay, well here it goes:

Season III

Having stopped the Wraith from reaching Earth and having achieved another failure with the Wraith retrovirus, the expedition faces its third year in the Pegasus galaxy with the Wraith still a threat and a new powerful enemy bent on destroying the expedition and Atlantis: the Asurans. The situation becomes complicated when an experiment gone awry drains their only ZPM, leaving them without a power source for the city's shields. Soon thereafter, they find a lost Ancient vessel and subsequently lose the city of Atlantis when the crew of the Ancient ship reclaims it. The SGC sends General O'Neill and Richard Woolsey to try to negotiate an agreement between Earth and the Ancients to allow the expedition back in Atlantis. O'Neill and Woolsey dial Earth and inform them that the Asurans (self-replicating nanobots) are taking over the city. They kill off the Ancient crew who reclaimed the city after 10,000 years. The main members of the Atlantis expedition on Earth disobey the orders and go back to the city, rescue it, and destroy all the Asurans. The season finale starts off with Earth launching a first strike against the Asurans who are building an armada to attack Earth. The Asurans counterattack by attacking Atlantis by means of a powerful beam weapon fired through a satellite housing a Stargate. As the last resort, the Atlantis team fires up the city's stardrive and escapes into space. The finale ends when the hyperdrive malfunctions, leaving the city flying through uncharted space with a day's worth of energy left in their sole ZPM and Dr. Weir critically injured.

Moving on to Season IV

The future appears bleak with the incapacitation of Weir and multiple injuries among the senior members of the expedition. With the city damaged, running out of power and drifting in space, cut off from Earth, the Atlantis expedition raids Asuras to obtain a ZPM and is able to travel to a nearby planet. Weir is captured by the Asurans and Colonel Samantha Carter joins as a regular and acts as the expedition leader.[11] She appeared in the episode "Lifeline" after helping to find and land Atlantis on its new home planet; however, it is stated that she has been ordered back to the SGC at this point. In episode 3, however, under the IOA's orders, Carter returns to Atlantis as the new leader of the expedition after Atlantis lands. Generally, the season focuses on the main antagonists the Asurans and the Wraith, as early on the Asuran base code is reprogrammed by McKay to start a war with the Wraith. Midway through the season the Asurans are seemingly destroyed, and the remaining episodes concentrate mainly on Michael's efforts against both humans and the other Wraith. Carson Beckett and Teal'c both appear in several episodes

Thus setting th stage for season V

Important Episodes to watch:

Season IV

Adrift Part I and II

Travelers

Missing

The Seer

Kindred I and II

The Last Man (Season Final)

I also just started watching Stargate Atlantis. I am currently on the 3rd season. The first answer was great. You might also be able to read synopsis of the episodes on the scifi network.

i believe that Michael set the trap and wanted it to look like they died but they would have been beamed aboard a ship instead