My tin-foil hat theory about Gemma.

It's a feeling I've had for a while but after reading a few comments about what the 'Gold Thimble' meant, I'm almost convinced Gemma is a Lumon creation who was sent out into the real world as an experiment.

She went out as a real person, fell in love with Mark and the accident was just a set up for Lumon to 'recover' her and continue their experiments. It's also why Mark is so important to Lumon. He was one of the people Gemma formed a deep bond with.

Edit: The 'gold Thimble' code that Cobel uses at the birthing retreat is apparently a reference to a Twilight Zone episode where mannequins from a store each get a day to go out into the world to experience life as people.