Ok. I'm a bit late to the game. I completely missed this series first time around. I just found this series on iplayer now and have just finished watching it, and like many, came on the internet to find out how the ending makes sense. Firstly, I just want to say I loved it, and wasn't Merlin aka Colin Morgan, great? I haven't looked at AI's take on it, because google AI often gets things wrong and it is much more fun trying to work it out.
So my take is this. You have Nathan and Charlotte living in the 1890's. Charlotte must continue living as she goes on to have a daughter who is Laura's (red coat lady) Great Grandmother. So if Charlotte survives, that part of the story of Nathan and Charlotte living happy together in the house with a new baby must be true. Nathan, leaves his bed to go downstairs to the seance and Charlotte is still in the bed.
So you have two timelines playing simultaneously. Nathan and Charlotte in the 1890s and Laura and baby in present day.
So in the 1890s Nathan has been wracked with guilt over the death of his son Gabriel who died by drowning at the house, all though not talked about, we know his first wife also died somehow at the house too, so he left to go to London where he buried himself in being a psychologist. He meets Charlotte there, falls in love, when his mother dies at Shepzoy, he goes back to sort out her affairs and it is Charlotte that persuades him to move back and take on the farm. Strange things start happening, he and various other people see a ghost with a book of light (Laura), other weird things keep happening. Nathan, who is foremost a scientist is sceptical at first, but with unresolved grief and guilt over his son, starts to want to really believe as that means Gabriel could also be a ghost and is on the urge of losing his mind, strange things keep happening and he gets the reputation of raising the dead.
Meanwhile, Laura, living in present day has a baby. She has been seeing a ghost of a little boy (Gabriel) and puts it down to post partum psychosis and checks herself into a mental health institute. Her Grandmother then tells her Nathan and Charlotte were her great great grandparents. More importantly, Laura's mum committed suicide when Laura was 3 months old because she also saw Gabriel but no one believed her, so she thought herself mad. Laura, now having this knowledge realises she isn't mentally ill, but is seeing the ghost of Gabriel and goes to the rundown Shepzoy to find him, to ask why she is seeing him and how he can help. We learn here, that Gabriel holds his dad responsible for not playing with him, so he went to the lake alone and more importantly not saving him when he drowned. We also learn that Gabriel is scared he is going to be replaced by the new baby and that he will be forgotten. The ultimate emotion is that his dad didn't love him. Whilst at Shepzoy, Laura sees the ghost of Nathan at traumatic points of his life, as well as Harriet who has just slit her wrists and scares her witless so she leaves Shepzoy in a panic.
From this we can concur that Gabriel is somehow stuck in the afterlife with feelings of being abandoned by this father, his father, Nathan is stuck in his present life with feelings of guilt and grief. This combination of such unresolved emotion and SOMETHING else at Shepzoy has caused the hauntings. What is the something else? We don't know, but various characters have left referring to 'something bad here'. We do know there was dreadful massacre by the roundheads in the 1600's which probably left a dark trauma in the land. (the reference to the soil being full of blood). After all the villagers and Charlotte witness that traumatic event, Nathans obsession with seeing Gabriel grows as he know has undeniable proof that ghosts exist. He pushes Charlotte away and is desperate to see the ghost of Gabriel, leading him to take magic mushrooms where he finally sees Gabriel's ghost, who asks him to join him and look after him by taking his own life.
So what Laura sees as ghosts and what Nathan sees as ghosts are each other at traumatic periods in their lives. (Laura running scared to her baby because she just heard a ghost, Gabriel, singing over the baby monitor, Nathan about to poison himself.) However, the timelines don't necessarily tie up. So Nathan is in the kitchen when he sees the ghost of Laura shouting at him to stop (killing himself) whist he is actually washing his hands etc. I think this was just to make it more thrilling, spooky, less predictable.
So going back to Laura, she is alive at Shepzoy, she comes across the ghost of Harriet in the dark, who has just slit her wrists, and is terrified, grabs the baby and leaves in the car, driving fast. She sees the ghost of Nathan, swerves, crashes and dies. Nathan in his timeline witnesses the car, because it is another traumatic event in Laura's life.
It's at this point Laura wakes up in the afterlife, back in the house at Shepzoy. Gabriel wakes her up by saying his dad is coming. He means to join them. She still thinks she's alive and understands that means Nathan will kill himself. So runs down to the kitchen and sees Nathan and runs in and shouts 'no'. She is still not in his timeline as she is now a ghost in her own time line, so Nathan doesn't physically see her at that point. (He saw that play out before out of context.) Because Nathan then disappeared she somehow appears to Charlotte and lets Charlotte know that Nathan is about to kill himself. Charlotte runs back to the house and saves the day. Gabriel finally appears to his father as a ghost (ie not under the influence of drugs), so Nathan finally gets to apologise to his son for not being there, saving him and tells him he loves him. That is what the Nathan and ghost of Gabriel needs, so Gabriel disappears to Nathan as that emotional conflict both of them is resolved.
Nathan and Charlotte can finally move on and be happy, Charlotte has her baby, they remain at Shepzoy. The farmers find Laura's crashed car buried in the bog. Because it's so weird they think it's the cause of the 'bad thing' at Shepzoy. (Now, I thought this was a bit weird, because up until then, anything from a different timeline appeared as a vision not a physical thing. I also didn't think it had fallen into a hole it just felt like a timeslip. If you can imagine a car coming off a road and not being moved for a hundred years it would finally be covered over with soil and vegetation, so that is what happened but weirdly went backwards). However, Laura sees them uncovering the car, at this point, she still thinks she's alive, on seeing the car she remembers the crash and she realises she died in it, and is stuck at Shepzoy, Gabriel appears to her and says she can now be her mum and look after him and also tells her her baby is safe as her husband is looking after the baby. Nathan witnesses them walking off as ghosts. Finally the lady with the light book and his son, hand in hand, so he thinks its all good and the hauntings will cease, that the weird object (the car) was the cause of the hauntings and it has all resolved.
Fast forward, Charlotte and Nathan living their happy new life together at Shepzoy in the 1890s. Nathan wakes up one night (Charlotte is lying beside him) as he hears a voice of another ghost from downstairs calling his name. He goes downstairs to witness a seance party is in process (looks like it's from the 1920's or 1930's). The people in the party are summoning Nathan, so we are seeing it from a ghost's point of view. He just sees a bunch of people in his living room having a party and calling him, and when he appears they ask him why he killed his wife. If we fast forward in time to another timeline of the 1920's/30's, and see it from the seance party's view, they are drunk they have decided to have seance after their dinner. They are shouting out 'is anyone there', 'Nathan are you there', then they get confirmation (as he appears at the bottom of the stairs) so maybe one of the party goers is a psychic and has a feeling. They then ask, 'Nathan, why did you kill your wife?'
This goes back to something else Laura's grandmother touched on, 'The 'Notorious' Nathan Appleby was your great great grandfather', and his local reputation as 'raising the dead.' So If you are living in a house in the 1920's knowing that a potential muderer and lots of bad things happening there you may well have a seance (it was big in the 1920s and treated as a parlour game.)
So! What a shame BBC cancelled the second season, because it was certainly written as if there was another series. From this, I would say the implication is Nathan murdered his first wife. But we will never know, it may be that he didn't and the second series would have played out that 'the bad thing' at Shepzoy made it look that way. Maybe it would have explained the bad thing or the massacre more. Maybe it would have explained that Nathan was grieving his wife's death so that is why he neglected Gabriel. Maybe the car that had been dragged out of the bog would have disappeared or become something more keeping with the 1890s, who knows. When you think about it, the family was wrought with tragedy. Gabriel, Gabriel's Mum, Charlotte's grandaughter (Laura's mum), Laura. What would have happened to Charlotte and Nathan? I thought it was a brilliant piece of writing, I would have loved that as a book. The only odd thing was the modern day car appearing as physical object in the 1890's. Maybe they just put that in to explain Laura's death.