How this will work...

Honestly, I have no idea how this will work.
The plan is to talk with as many iNGOs as possible and see if we can source someone to take over the project. That will include agencies like IRC, ICRC, Merlin, MDM, StC, WV, and the numerous nation-specific NGOs. We'll also talk with other MSF sections already in Liberia (MSF-France, MSF-Swiss, MSF-Belgium, MSF-Spain). There are lots of iNGOs in Liberia. We just have to find one to take it over.

The finding/negotiating part takes place at as many levels as possible. The country management team is working on it from the capital level, the Project Coordinator works on it at our local level, and the whole team works on exploring avenues whenever possible.
In an ideal world, we would transition the whole project to a single agency. That would include all four clinics and the hospital and also the specialized programs that MSF has implemented - vertical HIV, TB, SGBV programs on top of primary and secondary health. Given the depth of programs we support and the complexity of certain programs we have implemented, we would hand over pieces of the program if necessary to different agencies.
Ultimately, the HoM (Head of Mission) is responsible for the negotiations.

Potentially devastating. That's pretty strong phrasing. We of course begin by doing everything we can in case no other NGO steps in. Training, sustainable projects, guidelines, documentation, etc. Since the project was established, a part of the work we do is to implement our protocols and standards. I hope, after three years, that those things could be carried on whether or not we're here.

There's a secondary consideration when talking about pulling out, especially from a region like upper Nimba, where MSF is the only medical iNGO present. To put it bluntly, there exists a possibility that NGO presence here allows the Ministry to, well, ignore the region. Why would they expend energy and money and staff and supplies if an NGO will provide them?

I cannot say if that is the case. It's neither my place for analysis of that sort, nor is this the proper venue for any kind of assumption of that type. What I can say is that, in my limited experience, this argument especially in post-conflict countries which have experienced a distancing from the conflict, which have entered a phase approaching normalcy and increased infrastructure development and the like, is given weight by many different people. I suppose it's considered human nature to allow others to do your work for you if possible, and to ignore something that someone else is willing to take responsibility for. There exists a train of thought that some countries are fully capable of taking over NGO projects that are run inside their borders, they just won't do it unless they are left with no other option.

The long-term goal of most humanitarian agencies is (well, "should be" in my opinion) to leave. Eventually, you hope to see governements and ministries and communities independently capable of caring for their population, whether that's schools or hospitals or roads. MSF has a charter that indicates we would, usually, leave before others - as an 'emergency' agency, MSF's doctrine is to pull out as soon as the emergency is over. Granted that's not always the case. Many MSF projects have run for years after the emergency is over - a reticence born, I presume, of the entirely natural bad feeling you get from 'abandoning' a population in distress. Certainly we are experiencing some of that hesitancy ourselves.

Not an easy position for any of us.