I liked this scene, and I really liked what it did for the relationships and mythology because our idea was that CSM really had three sons. He had Mulder, who was the heroic but rebellious son. He had Spender, who was the weak son, whom he thought he could manipulate. And then Krycek, who was not biologically his son but was certainly a protege - who wanted his love, his approval, who was the only one who really wanted to carry on his mantle. And CSM would not have him.
Tragically, for CSM, because if he'd accepted the alliance with Krycek, everything might have turned out differently. But he didn't feel that Krycek was worthy.
And it's really a nice thing for Krycek's character and the whole story because there's some vulnerability to Krycek here that you really never get to see otherwise.
--Frank Spotnitz, commentary for deleted scenes from Two Fathers (6x11), The X-Files