Much to my surprise, "The Council" was a tight and entertaining story, where the characters behaved in a logical manor.
The reptillians and insectoids seem to have taken power, and are now bent on destroying earth in the name of their guardains (and a reptillian led Xindi empire), and it was good to see the aquatics side with the arborials and humanoids against them. The death of Degra was a little surprising, but it did seem to me it would happen when the reptilian leader arrived unannouced at his quaters.
My guess as to why Hoshi was captured at the end is the Reptillains want to use her abilites to get the final code they need to activate the weapon.
It's a shame it took till this show's seeming end to produce this kind of episode, which was good and made sense. There may yet be hope for the show, they are still saying season finale, not final episode.