Binge watched this weekend & came on threads to see theories!
I will now vomit my theories up on the page! 
I think Sam, the brig & driller are all in it together.
I think Reed knew nothing of it all until he was called in to try and help Sophie when she got sick, because he was a medic (they tried to use the Iraq thing to blackmail him into silence, but it backfired on them when he killed himself at the horror of what they'd been up to).
Him killing himself and Sophie being so ill made them come up with the 'plan' of her being Alice.
'Alice' (Sophie) definitely flinched in the hospital when Sam tried to take her hand, and again in the kitchen at home when he asked if she wanted a cup of tea.
He also said 'good girl' in the shed & she looked fearful of him.
He was also adamant that she was Alice - every time Gemma expressed any doubts he shut her down quickly and kept saying 'we've got her back, that's all that matters now' or similar.
Lena was drillers daughter I think, and Sam gave driller's DNA instead of his own to 'prove' the body was Alice.
I think he wasn't in on the fire plan though, because otherwise he wouldn't have dashed in to try and save her like he did - I think he thought it was a tragic accident.
No idea if he knows that Alice is actually alive though tbh - I think he just might be in on the Sophie & Lena part of the abuse ring.
Not sure though...
Either way, am v excited to see the last episode - I love these series - brilliantly written!