This second season improves on the first. In the last episode of the first season Jack had disappeared when he heard Doctor Who's Tardis in the area (the story which is continued in DOCTOR WHO The Third Series). It's now some months later and everyone is pissed when he returns since they feel as if he had abandoned them.
And there are two more time-travel incidents, one that has Jack meeting the real Jack Harkness during WWII. This is the soldier whose identity he stole since the guy was killed in action. And that day, Jack realizes, is the following of this meeting. In another episode, a young soldier is brought out of deep freeze one day a year, for an undisclosed reason, and it turns out that Tosh is in love with the guy. When a time-rift opens, that needs to be closed, it's up to this soldier to help close it. However, this means he'll die when he's sent back to the fighting.
In one of the more intriguing episodes, Owen is shot and is resurrected by Jack, via the "Resurrection Glove" seen in the first season. Only it doesn't bring him back to life-- so he's basically dead but still walking and talking. He starts to be taken over by an entity that has come from the blackness but they manage to make it go away. However, Owen still has to deal with "living" as a dead guy. For example, he breaks his finger--which means it will never heal. This does have an unforseen side effect in that it makes him less an asshole--and he and Tosh (who has a crush on him) become closer.
Gwen gets married, though she's bitten by an alien shapeshifter the night before and wakes up to find herself nine-pregnant with its child. There's lots of running around as the alien mother is in disguise as one of the wedding guests.
In one of the season's more disturbing episodes, Gwen is called in to help find a fourteen year old missing boy by her former police partner and discovers that people are being sucked away by the rift. Since aliens, like the "Weevils" are constantly coming in through the rift, to the Earth, it only makes sense that the opposite has been happening. She wants Jack to investigate and somehow stop this but he's adamant that he won't. She comes across a hidden Torchwood facility that has been caring for these people that have begun to return. They are all insane and are all damaged beyond repair.
Captain John Hart (James Marsters of BUFFY and SMALLVILLE) returns and he sets explosive devices in a building that the Torchwood gang is investigating. Jack discovers, to his horror, that this was all planned out by his long lost brother. In a flashback in a previous episode we saw how Jack's colony was invaded and attacked by aliens and how his brother was adbucted. Now the sibling is evil and wants big brother to pay for all those years of torture.
The season ends on a BIG down note as not one but two of the main characters are killed off. I wasn't expecting that. And just when you think it can't get worse for the remaining characters--Season Three comes along....