I feel I should note a few things about where I think they're going with Torchwood....
The hand in the jar? The one the aliens cut off the Doctor during the Christmas Day Invasion. And I reckon Jack's studying it to find out how he's able to regenerate.
Then there's the matter of the 'giving life' thing, which we've seen the Doctor do in Rise Of The Cybermen.
And we know from Doctor Who that he's a time traveller, which means he's brimming with the time-radiation used by the Daleks to power certain technology and which probably comprises the bulk of the make-up of the Time Vortex.
So I reckon when the Bad Wolf (the Time Vortex inhabitting Rose) brought Jack back to life in the Season 1 finale of Doctor Who, she did one of two things: She either over-did the energy and infused him with ****load of time-radiation, effectively making him some kind of demi-God, or she flat-out made him a Time Lord.
I'm hoping it was the latter, and they explain his presence in present-day Cardiff as him having used some half-assed TARDIS to skip across the Rift.