Didn't Durandel say in m2 on the fourth level (I think) that the S'pht were attacking you because they were pretending that they were still under the control of the Pfhor cyborg the player killed in m1. And they were doing this so th pfhor would not realise they were not under his control and kill the S'pht.
If this is so then why would the pfhor send their super important S'pht controller into deep space on a lone ship instead of keeping him safe on thier homeworld? I dought they're that stupid.
Also if this is so then why would they think he's still alive if the ship he was on is flying around the system kicking thier asses?
