the war with the xindi is over. not a spoiler since this happened in the last episode of last season.
the reptiles launched the "weapon" at earth, the Captain followed it with some "good" xindi, while the enterprise was off destroying the spheres (which supplied power to the weapon, or something). the Cap managed to destroy the weapon in person with some other Good Guys. the other Good Guys were able to transport off the weapon before it destroyed, but not the Cap. everyone assumes he is dead, they head for home. upon reaching home they discover they're in the 20th century, which starts off episode 1 of this season...