The missile contrails were from ICBMs. I suspect that they were either launched intentionally as a retalitory strike against the (still unknown to us) aggressor nation, or they were launched automatically against their pre-programmed targets as part of a "fail-deadly" response.

"Fail-deadly" is a military strategy concept whereby a guaranteed, overwhelming response will automatically befall an attacker by setting up a response system that requires intervention by an operator to prevent it from being carried out. Sort of like a dead man's switch, it is designed to provide authorization for a retaliatory strike even if the existing command and control structure has been neutralized by a first strike.

Of course, for a "fail-deadly" strategy to work, there can be one and only one assumed aggressor (during the Cold War, that would've been the USSR), since the ICBMs would have to be pre-aimed at their targets, and there theoretically wouldn't be anyone around to re-aim them if the aggressor nation was someone else. In the world of 2006, I don't know if that sort of an assumption is valid any longer. More to the point, if the ICBM launches we saw at the end of the episode were indeed part of a "fail-deadly" response, then I believe it to be entirely likely that the response would take out someone OTHER than the actual aggressor. I think it much more likely that the C&C infrastructure is intact, and that the strike was a limited response against a specific set of targets.