Creeping Death, Part I 
Summary: St. James comes into the infirmary with a case of the unexplained illness. The medical crew is horrified as his state rapidly degrades.

 
Creeping Death, Part II
Summary: The corpse of St. James is brought out for autopsy. It reanimates, and tries to kill both the Doctor, the Second Officer, and anyone else that stands in its way. 

 
Splitting Heirs
Summary: Mekara arrives on board Station 419. Her true purpose for being on the station is soon discovered as she reveals that Lt. Nevaren is her half-brother. Arguments among the chain of command culminate in DNA sampling..

 
Against Orders, Part I
Summary: TThe crew defy orders to rescue Commander Balin, who has been trapped on Betazed. The crew (and some accidental hitch-hikers) travel to Betazed using the artifact. There they must dodge Jem'Hadar patrols, and eventually end up at a cottage currently occupied by a Cardassian Gul.

 
Against Orders, Part II
Summary: The crew defy orders to rescue Commander Balin, who has been trapped on Betazed. The crew must figure out to do with Halev, the Cardassian Gul, as well as figure out where to find Ensign Tyler and Commander Balin.

 
Make Us Strong
Summary: Pakleds steal the USS Aegis for purposes unknown.

 
Hiccups
Summary: Strange debris is pulled from the anomaly.

 
Proclamations of Goddess
Summary: Siethni'kek, an insectoid creature from Siinoga, confronts Ambassador VuQ'cheH with the news that the Siinogans have invaded the Klingon colony of Bak'TUR.

 
Irdosian Fireworks
Summary: The crew travels to Irdosia to study the population there, and end up breaking the prime directive.

 
Damage Control
Summary: The crew must try to minimize breaches of the Prime Directive during the Irdosian mission.

 
Protests
Summary: The crew must evaluate Occa as a suitable candidate for Federation Membership. However, all is not as it appears on the once-isolationist planet.

 
War Games
Summary: Nausicaans have captured the crew of the USS Aegis. Can the crew figure out how to escape before there is a mutiny?

 
Ghosts 'n Goblins
Summary: Strange events have been occuring at a colony's mine and the crew must discover the source.

 
Arsenal
Summary: The crew discovers that the Siinogans are able to produce Ketracel White, and a deal with the Dominion is underway.

 
Bug Hunt
Summary: After the Siinogans are blockaded, a science team accompanies Commander Balin to retrieve a Siinogan artifact.

 
Hypocrisy
Summary: The crew takes a runabout to Utopia Planetia shipyards to confront Hendricks and T'shon, temporal criminals.

 
Valley of the Shadow of Death, Part I
Summary: When the Aegis departs for a final confrontation with the Siinogans, the Dominion makes a surprise attack on the station.

 
Valley of the Shadow of Death, Part II
Summary: This is the same episode as I, but from the perspective of the Lower Decks.

 
Ancient Shadows
Summary: A small away team is sent out to investigate anomalous readings of misplaced ores from a remote planetary system on the fringes of the Dulcais sector. They find the source of the readings, along with a mystery. What was once a thriving civilization, evidently of Vulcan stock..that simply dissapeared.

 
Flea Circus
Summary: Tanol's Ttraveling Zoo visits Station 419. The crew finds some exciting, and shocking exhibits.

 
Not As We Know It
Summary: A strange, water-based life form shows up at the station.

 
Future's End, Part I
Summary: The crew is thrown into the dark future, only to find that the anomaly is gone and the station and Aegis are both dead in space.

 
Future's End, Part II
Summary: The crew is sent to the future, only to find the horrors of the Lithians have come to pass...

 
Future's End, Part III
Summary: The crew is sent to the future, only to find the horrors of the Lithians have come to pass...

 
Guard Duty
Summary: Three senior officers encounter different timelines as they perform guard duty of the artifact.

 
Revelations
Summary: Evans reveals that he has the ships logs from the Future Aegis (Future's End, Part III). Balin calls several meetings regarding it, and drops a bombshell of his own.

 
Laco's Parents
Summary: The crew rescues Laco's mother from the clutches of the Cardassians.

 
Bite of the Mosquitoes
Summary: The crew must defuse a tense situation between two technologically primitive space forces. And destroys them instead.

 
Exile
Summary: The crew tries to rescue a ship that is en route to the station from Occa, under heavy pursuit. They discover that the Occan people have had a revolution and have ousted the government of Occa.

 
O Betazed, Part I
Summary: Anomaly's second season finale. The USS Aegis is assigned to the space force that is retaking Betazed from the hands of the Dominion. Occurs simultaneously with Part II.

 
O Betazed, Part II
Summary: Anomaly's second season finale. Part of the crew is assigned to the ground force that is sabotaging the planetary shield network. Occurs simultaneously with Part I.