Zuul’s "son" From what DNA was he created? He has nanobots in his blood that Zuul put there, for use at a later time. She can enable them (or they might enable themselves) to give him strange abilities.
Possibly spliced in fragments of many species’ DNA, in an attempt to enable abilities within him. One idea is that he’s multiple souls. Nanobots in his body form the nodes of a larger computer – a picoweb – the nodes of a soul-bearing computer. Basically, there is another soul coexisting in his body distributed throughout the nanobots’ web.
Another idea is that the picoweb begins to malfunction, and starts absorbing additional souls when he is near them during their deaths. More and more voices in his head!
StratCo designed Matt to be "ultimately compatible" with cybernetics. They designed a brain that resembled a human’s but is a "biological computer."
Years ago, Zuul hacked into StratCo’s computers (a hobby of hers) and stole the plans for the "computational human." She modified the design a bit, adding a real human soul, and infusing him with unique nanites of her design.
StratCo was aware of the breach, but did not know the culprit for years. (StratCo contracted Boris to track down the hacker responsible. Boris deduced that it was Zuul, confronted her, and she paid him off.) However, after seeing Matt on live television recently, they recognized him, thinking that someone must have adapted the design into a soldier.
They send several units (out of 8) ("evil Matts") after him, to bring him back.
The closest thing Matt has to a "father" is Ron Davis, though DNA was taken from many, many sources and spliced with the original genome.