Kyle was supposed to be abducted, brought to the future, and enhanced so he could serve as the liaison between the future and the present...Especially between the future and Tom (his father) who is supposed to assist the 4400 in keeping the Oblivion from coming to fruition.
However, Shawn went and done fucked things up by trying to save Kyle. Instead, Shawn got abducted...
Where things went from there...I got kinda fuzzy. Shawn reinvigorated Kyle...who wasn't Kyle, but was the Kyle from the future (I think.)
So, when Asshole shot Kyle...he shot future Kyle. And in that ensuing ball of light, normal Kyle was returned.
I think.




