I have been wondering where they can possibly go with S3.
After all, the innies have wreaked havoc in Lumon. They’ve ruined the experiment with Gemma; they’ve set Gemma free; they’ve killed Drummond; they’ve stirred up rebellion in both the goats and marching bands departments. So they are hardy going to be popular, are they.
When Jame Eagon visited Helly in the MDR room he was saying how he used to see Kier in Helena but didn’t any more. Then he went on to say how he did see Kier in Helly.
Which sort of implies to me that he prefers feisty Helly to his “fetid moppet” of a daughter Helena.
So… maybe he’ll have a permanent overtime contingency on her, so she is always Helly, even outside of the severed floor? I can well believe he’d happily “kill” his own daughter!
But of course Helly on the outside would probably want her innie friends… so would she insist that they were all innies all the time? And then Gemma and Devon etc would have to fight to get the outies back?
I am almost certainly completely wrong though!
I am really interested to find out what Lumon is ultimately trying to do. They are trying to create completely emotionless, compliant workers maybe(?)
I was convinced that they were never actually going to kill Gemma - right up to the goat scene where they were going to sacrifice the goat and entomb it with Gemma. And now I just don’t know any more! Hopefully all the semi-religious stuff will be explained. Just pleeease don’t do a “LOST” on us, scriptwriters!
I suppose we now have a couple of years before S3 airs 
which is a long time for everyone to be musing on plots and theories(!)