It didn't entirely make sense (about par for Torchwood) and usual for RTD it was all solved at the end by letting the hero find the right button to push which destroys the enemies. (At least they didn't actually have the button installed in their base's control console, this time).
Oh and of course when Torchwood HQ gets destroyed (again... BTW I forgot to watch carefully enough - did Canary Wharf turn up in the London Docklands stock footage?) they manage to reboot themselves by installing "the torchwood software" from "the torchwood servers" which presumably are stored in some robust off-site data centre in Maidenhead which nobody thought about trying to hack into...
"Will you remember me in 1000 years?" asks Ianto - well, of course he will. Jack already has through 2000 years of his personal timeline in the events of the season 2 finale (clearly the writers have not considered previous events - the entire cast have completely forgotten about Tosh for example).
What I found most disappointing was that it was, essentially, a five hour exploration of a dilemma which they'd already done in the first season. They could probably have made a competent two and a half hour movie out of that plot, but this miniseries felt distinctly padded.
Not for the first time, I'm left not entirely certain why I bothered to watch it.