10 Battlestar Galactica Twists You Never Saw Coming

At the conclusion of Kobol's Last Gleaming (the two-part season 1 finisher), humanity looked to be in a pretty dire situation. Starbuck had absconded back to Caprica, while the landing team sent to Kobol had been shot down by the Cylon's guarding it. While Boomer and Racetrack had successfully destroyed a Cylon Basestar, this was largely because the Cylons let Boomer do it. Then Boomer and Racetrack report to Adama to be congratulated.

And Boomer shoots him twice.

We already knew that Boomer was an undercover Cylon, we already knew that she was struggling with her sleeper identity. But her confrontation with dozens of copies of her on the Basestar, it seemed that she was able to command her own destiny. Boomer seemed to be able to make her own decisions. Then she shot the Commander. This would set up the beginning of the second season as a struggle to maintain order.

While the audience was expecting some kind of cliff-hanger for the end of the season, this one was a double-tap to the chest. Well... stomach.