When we last saw Alex Krycek, he appeared to be working against the Consortium. He blocked the export of nanotechnology to Tunisia, after all, and the Consortium is known for their connections to Tunisia. Well, scratch that. In "Two Fathers"/"One Son," Krycek is back to being a loyal member of the Consortium.
We first see him giving a lecture (complete with slideshow) to the Consortium elders, in their New York City headquarters. He's not just an assassin or a driver now - he's now a white-collar Consortium flunkie, wearing a suit and everything. (No tie yet, but he was wearing a suit.)
He's still doing some driving, though. CM wants his son, Jeffrey Spender, to kill a rebel alien who has impersonated one of the elders. He has Krycek drive him there. Krycek apparently has orders to look out for Spender as well. When Spender's reluctance and inexperience allow the alien to get the upper hand, Krycek saves him, stabbing him in the neck with his trusty plam.
Krycek then takes the opportunity to tell Spender that his father, CM, is the one responsible for the years of abductions and tests done on his mother, Cassandra. Outraged, Jeffrey runs out, hating his father and determined to protect his mother. Obviously, this is the result Krycek wanted, though we don't know why.
When the Consortium abandons their New York City offices to go with the aliens, Krycek stays behind to wait for Spender. He tells Spender where the others went, and that CM has gone to get Cassandra. Krycek then goes to Fort Marlene, bent on retrieving the alien fetus kept in deep freeze there. He's dismayed to find out that the alien rebels got there first. The fetus is gone, and another Consortium scientist is dead.
Though it seemed in "The Red and the Black" that Krycek might be working with the alien rebels, it seems clear now that he is not. If he were, he wouldn't be so furious to discover that the rebels have stolen the fetus. And why did Krycek want it anyway? It was useful for two reasons: to make alien/human hybrids, and to make a vaccine against the Black Oil. Cassandra was the perfect hybrid, and Krycek didn't seem to have much interest in her, so presumably he wanted the fetus in order to make a vaccine. Perhaps Krycek is member of the Bill Mulder faction of the Consortium: those who want to fight the colonists.
Whatever Krycek wanted, he is thwarted. As he stalks angrily through the corridors of Fort Marlene, someone calls his name. It's Spender, who came looking for his mother and found Marita Covarrubias instead. He wants Krycek's help in getting Marita out of the facility. Krycek tells them it's all going to hell, and walks away, leaving them there.
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