The second season of Stargate SG1 contains 22 episodes. Note that this will spoil the ending of season 1, and the very basis of some plotlines may spoil some of those that come before them. I'll do my best to keep such spoilers to a minimum.
1) The Serpent's Lair
SG1 is trapped on one of Apophis' attack ships at Earth's door. They're ready to blow this thing out of the sky, but that still leaves the other ship poised for attack. On Earth Samuels, at the behest of Kenzie and Maybourne, is ready to blast the ships with special warheads and won't listen to Hammond's wisdom on the matter. But SG1 is not beaten yet, not with Master Bra'tac as an ally.
2) In The Line Of Duty
An air strike on a village leaves plenty wounded. As Sam performs CPR she is infected by a Goa'uld who claims to be a Tok'ra, a friend. But if so then why did she act so violently? If she's lying there's the matter of not being able to remove the parasite, if she's telling the truth there's an assassin out to kill her. It's lose-lose.
-This obviously introduces the concept of the Tok’ra, but there is a lot more to come.
3) Prisoners
SG1 is sentenced to life in prison by an alien race. Condemned to an underground cave with no way out an elderly woman may be their only ally in escape. Meanwhile Hammond attempts to negotiate their release. Their efforts will lead them into the presence of the Destroyer of Worlds.
4) The Gamekeeper
A new world - beautiful and technologically advanced: SG1 finds themselves unwitting residents and transported to troubling historical events in their lives. They are forced to relive the deaths of friends and family over and over. Is this a chance to set things right or just a twisted game?
5) Need
SG1 finds a naquadah mining operation. Daniel stops a suicidal princess resulting in the team's capture by Jaffa. The team is sent to work in the mines except for Daniel who has the chance to convince the ruler to free his friends. Problem is he is succumbing to the addiction that the healing sarcophagus causes while his friends are worked to death.
-This episode really examines the use and effects of the sarcophagus technology: its addictive properties and its affects on the mind. It is an important piece of the puzzle in understanding the evil of the Goa'uld and the difference of the Tok'ra. It also puts a stop to what I’ve seen as a writing weakness, the overuse of the sarcophagus to get out of tough situations.
6) Thor's Chariot
Thor's people send Earth a plea for help. SG1 responds to find a Goa'uld invasion. Their only hope is finding a secret weapon hidden by Thor.
-This is the first revelation of the true nature of the Asgard, and sets up what will become one of the most important races Earth meets on its travels.
7) Message In A Bottle
SG1 brings home an alien device found on a deserted planet. When it activates they attempt to throw it through the stargate, but it lashes out impaling Jack against a wall. They can't pull him loose or sever the arm that holds him. As he slips towards death an unknown organism begins infecting everyone and everything in the base leading to imminent destruction.
-This proves that Anderson can play pain and emotion as well as all the odd stuff he's done before.
8) Family
Teal'c's son has been taken by Apophis. SG1 mounts a rescue mission, but in the course Teal'c finds his wife married to another and his son harboring deep hatred towards his "deserter" father.
9) Secrets
It's time for Daniel to return to Abydos as arranged. He finds Sha're there pregnant with a human child by Apophis. This is huge, for one because Sha're is temporarily in control of her body and also because the child will possess all of the knowledge of the Goa'uld which could be invaluable in the fight against them. But Apophis will be here soon to collect his progeny - future host to his parasitic self. Meanwhile, Sam travels to DC and is reunited with her father. He wants to get her into NASA and can't understand why she is refusing. Jack is also in DC, but he's at odds with someone else: a reporter with just enough knowledge of the stargate to be dangerous.
-Chris Owens (well known to X Files fans) guest stars.
10) Bane
Teal'c is stung by a giant bug on a strange planet. Even his symbiote can't fight what it's doing to him: reconfiguring his DNA into more of these bugs. Maybourne wants to experiment on him,but Teal'c quickly escapes in a crazed frenzy. As Jack races to save his friend research suggests that failure to stop him will result in a swarm of bugs capable of wiping out life on Earth.
11) The Tok'ra 1
Sam now has dreams of the Tok'ra and insists on trying to find them. Sam suggests an alliance, but the Tok'ra don't think the Tau’ri (Earthlings) worth it. In the middle of negotiations Sam gets word that her father is dying, and she, the one person that can relate to the Tok'ra, has to return home.
12) The Tok'ra 2
Things haven't gone well with the Tok'ra due largely to Jack's distaste of their parasitic nature. Is there no human being willing to be a host? Without such a goodwill gesture the Tok'ra will not even consider calling the Tau’ri allies. On Earth, Jacob Carter slips closer to death while Hammond has to decide how to handle both situations.
-This is a pivotal moment shaping many episodes to come.
13) Spirits
While searching for a missing team SG1 runs across a strange tribal people similar to Native American cultures. The people are willing to talk trade with SG Command, but they can't promise the cooperation of the spirits that protect them. The U.S. government decides to swindle the simple folk, but they have gravely underestimated the power there, and it may cost the entire population of the base their lives.
14) Touchstone
SG1 finds a civilization that can control the weather with a small device. On their return trip they find that the device is missing, and the people are blaming SG1. The team must unravel the mystery before the inhabitants of the planet are destroyed by the uncontrolled weather conditions.
-Maybourne and the NID have appeared in previous episodes, being actually introduced last season, but this is an important moment of revelation which does a lot to shape their future appearances.
15) A Matter Of Time
A black hole opens up with SG10 trapped on a nearby planet. When SG Command connects to assess the situation the power of the gravity well begins sucking Earth through the wormhole.
-This is one of my favorite episodes. The enormity of dealing with something as powerful as a black hole and its effects on time and space is fascinating. I'm no expert by a long shot, but I have read Stephen Hawking's theories on black holes, and I see a lot of research in the theories presented in the episode. It was interesting to see how such a phenomenon might actually affect situations around a living being.
16) The Fifth Race
Daniel may have tracked down some allies of the Asgard so SG1 sets out to make contact. While there Jack is grabbed by a strange device and shortly thereafter begins acting strangely. It seems they have stumbled across the Ancients, and their knowledge has been downloaded into Jack's brain. It's more than his mind can bear and will kill him if they can't do something.
-This is a continuation of the ideas set up in "The Torment of Tantalus" creating more mystery around the Ancients but also looking favorably on the human race and our potential.
17) Serpent's Song
Apophis is dying and begging for help from the SGC since he knows the humanitarian nature of the Tau’ri. Jack is uneasy but gives him sanctuary incurring the wrath of the system lord who wants Apophis for himself.
18) Holiday
SG1 stumbles across an old hermit that once posed a threat to the system lords. Now he's just a crazy old fool. He proves to be crazy like a fox and more innocently dangerous than the team could have guessed. He swaps consciousness with Daniel, but, thanks to his previous babbling, nobody believes the old man (who is now really Daniel) when he tries to explain what happened.
19) 1 False Step
The team is testing out a new long-range reconnaissance plane which crashes unexpectedly during its test run. During retrieval they meet a human-like race with virtually no communications abilities. The people start dropping like flies all of a sudden right before Jack and Daniel start acting strangely. SG1 may have inadvertently just killed an entire race and put themselves at risk to boot.
20) Show & Tell
An offworld visitor somehow overrides the iris controls and enters the SG base. It's a young boy (who X Files fans will recognize as Gibson Praise) who claims to have warning of an attack from an invisible enemy. He also claims to have an invisible mother. Jack and the others can't decide if he's a few cards short of a full deck or just trying to get attention.
21) 1969
SG1 finds themselves in the past, Earth's past, 1969 to be exact. They are detained by Cheyenne Mountain's current security under the suspicion of being spies. Their only hope is an unlikely ally, and even with his help they still have the challenge of figuring out time travel and doing it without destroying the past.
22) Out Of Mind
Jack wakes from a cryogenic sleep in 2077 to learn that the rest of SG1 is dead. He was frozen by another unknown race and thawed only due to the recent onset of the proper technology. As he tries to remember what happened to his team we end up with a clip show similar to "Politics" except that this one has more story.
-It’s surprisingly slow for a season finale, certainly far short of season 1.