S1:E26-S2:E1: Shockwave (Parts I & II): Tragedy strikes when the Enterprise Crew stops to visit a mining colony and the away team accidentally ignites the planet's atmosphere, incinerating the entire colony.
I know what you're going to say...I'm cheating, this is a column on Season 2 and here I am, promoting an episode from Season 1, but since it's a 2-parter and you really need to see the first part!
In another pair of episodes centering around the Temporal Cold War, it's revealed that a cloaked Suliban vessel planted a device on the shuttlepod that Captain Archer and his away team were on their way down to the surface in. This device is what set the atmosphere of the planet ablaze, and with the help of Cewman Daniels from the future, Captain Archer and his crew are able to solve the mystery, but not before Starfleet decides to scrub their whole mission.
However, when the Suliban come to take Archer prisoner in retaliation for infiltrating their ship to find proof of Enterprise's innocence, Crewman Daniels pulls the Captain from his time into the future, which has catastrophic results to the entire timeline. Archer's absence from his own timeline erases the United Federation of Planets altogether, and Crewman Daniels & Captain Archer must work together to find a way to send the Captain back to his time without the use of any 31ˢᵗ Century technology.