The first time we saw Krycek and WMM together was at the end of "Patient X," when WMM captured Krycek. Krycek had been trying to arrange a deal with the Consortium through WMM. WMM realized that Krycek must have a working vaccine against the Black Cancer, and insisted that Krycek hand it over in exchange for his freedom. He did, and WMM tested it on Marita. It worked. Eventually.
WMM was in disagreement with the rest of the Consortium over the fate of a captured alien rebel. They wanted to turn him over to their alien masters, his enemies; WMM thought saving him was humanity's best chance of resisting the alien invasion. So WMM sent Krycek to convince Mulder to rescue the alien rebel. And Krycek did it, even though he didn't have to. Once WMM set him free, he could have just vanished - but he didn't. Perhaps Krycek has some strange sense of honor, or maybe he really believed in WMM's cause.
And maybe Krycek owes WMM something. Thanks to Mulder, WMM was the only Consortium member besides CM who knew Krycek was locked in the silo. Perhaps WMM was the one who let Krycek out.
In "The End," Krycek, previously WMM's prisoner, is now seems to be his protege. He's sent to retrieve CM from his cabin in the wilderness, then spends the rest of the episode serving as WMM's driver and bodyguard. But he's not just WMM's errand boy. After CM does what they retrieved him for - captures Gibson Praise for them and turns him over - Krycek says, "I got a nice, straight shot." Pointing out that it would be easy to kill CM. WMM demurs, saying, "No. He’s useful. And you may need him in the future." Not "We may need him," "You may need him." As if he's grooming Krycek to one day take his place.
This is strange, since they were at such odds in "Patient X." Maybe WMM really was the one to rescue Krycek from the silo; if they had that kind of previous history together, it might explain why they managed to reconcile so quickly after the events of "Patient X" and "The Red and the Black." Or maybe WMM, growing old and increasingly on the outs with the rest of the Consortium, suddenly realized that he needed a successor - soon. (Or maybe Krycek was just really grateful to WMM for setting him up with Mulder in "The Red and the Black." :-)
We'll probably never find out. WMM died in a car explosion in the X-FILES movie, and took his plans for young Alex with him. However, in "Two Fathers" and "One Son," Krycek appears to be well established with the Consortium, lending credence to the theory that he was WMM's heir or protege.