I'll voice others and say that this was a wonderful ending. It's conclusive but unresolved at the same time. It has this realistic element that not everything has worked out but, eventually, it will somehow. Which is why I liked how you wrote this, particularly the ending piece; they aren't on the same wavelength regarding what's being done with the Company and Mohinder's involvement, but have acknowledged the problem and will try to figure things out as it goes along. This is something that all relationships go through when an obstacle comes in between two people, and it fits perfectly here.

In short, nicely done. :)