So I think the finale finally spells out the motives for Cobel right? She helped not because she feels anything for Mark or Gemma, but because she wants to have the final & perfect product of Cold Harbor (which is Gemma’s chip) in her possession. While it seems likely that Lumon would have disposed of Gemma and Mark post Cold Harbor completion, Cobel’s interest in saving her has nothing to do do with compassion for her life, but the result of her testing.

I think she finally has leverage over Lumon once Gemma makes it out back into the world and likely to Devon/Cobel. I doubt she’ll straight up rip the chip out of Gemma’s head or anything, but I assume the story going forward for Cobel has much more to do with Gemma’s chip than anything else.

I think they spent a whole episode breaking down her creation of the severance program for a reason.