SPOILERS....
I'm still not convinced PARIAYUH is Sgt. Cross. For one, Sgt. Cross is in the military and the military wouldn't knowingly let an infected join their ranks. Second, at the end, he turns into a Supreme Hunter which you've killed one of those before (spawned out of MOTHER after you inject something into her). I think the Supreme Hunter consumed Sgt.Cross sometime after the indoor battle becoming him. At this point, Sgt. Cross/Supreme Hunter starts contacting you and manipulating you. Both times after you kill the Supreme Hunter, you see a cinamatic with a hand coming out of a puddle of virus. Both times, you fail to consume the Supreme Hunter and only kill him (as confirmed by the Web of Intrigue).
The question is: what is the Supreme Hunter? It has intelligence and doesn't need to be connected to MOTHER to function (not part of the hive mind). At the same time, it spawned from MOTHER so there has to be a connection.
I think PARIAYUH might still be in captivity or, going out on a limb here, maybe Alex Mercer was PARIAYUH and BLACKLIGHT mixed with PARIAYUH to make him what he is. This seems to be confirmed when Green says "I am your mother."