Yes, I know.
It transpires that Sam's job is to get Gene booted out of the force. If he doesn't, Gene goes on to commit a dreadful atrocity that has repurcusisons for the British police and government.
In the last episode, Sam does get Gene banged up inside and has the chance to return to 2007.
But he refuses, choosing to stay with the WPC who he has fallen in love and lead the team into the new modern style of policing.
It backfires. Gene has a very long arm, and uses his contacts to see that Sam is shot dead.
In the last few scenes, Gene is released from prison and reinstated on a technicality, Sam is dead in 1973 and the wpc is crying. The tv announcer states that Sam's (2007 version) has had his life support switched off.
Then we hear the flatline tone.
In the spin off, we see the atrocity that Sam was supposed to prevent.