Is the skull from the Mass Grave with the bullet hole, which turns out isn't a bullet hole at all!
Was brought to the Orchid to find out how he died. There is something there which allows communication with the dead. This will also turn out to be the source of Miles' powers.
He looks like an Other. Given the location of the Swan is in hostile territory and the Others seems fully aware of everything happening on the Island it may be possible that part of the truce includes co-operation between the Others and DHARMA to build the Swan. The reason for this is not clear however.