The Architect saw he feared a lot but much of it stemmed from one thing: failure; failure to save his home, failure to his goal of helping others, failure to stop this deitic being.
But that fear was being combated by resolve and determination that no matter what happens, Dr. X would do everything he could to try and stop the destruction of the Multiverse.
He didn't really seek to control the Energies, more to help them reconcile with one another and to try showing them that total destruction wasn't wholly needed, Kreel was the root of much of the unbalance and stopping her would help pave the way to the Multiverse having a shot at harmony and the Energies being free to 'sing' their song together as they once did, maybe even make a more beautiful one.
"I may not understand them completely but I know they are a family driven apart by clashing personalities and a betrayal; maybe you caused that betrayal so long ago or maybe you didn't but I'm fighting not for myself or even my people." Dr. X said, "I am fighting for what's right and for all who seek to make the best of their own lives and to uplift the lives of all others around them. By trying to erase everything, you are my enemy and I will do all I can to try and stop you, even if I die; I die knowing I fought for what is right: for life and harmony, with all the strife and conflict of differing opinions and views that help to create that harmony."
"Harmony isn't all one thing or another, but the result of the whole being greater than the sum of its parts and all having the opportunity to help and benefit the whole." He said, trying harder to invite the Energies themselves to help them, to try harmony...even if it takes a long time to achieve.