Ironically enough, the disappearance was partially due to Jack's actions.
One day, having followed Jack into the forest behind their home, Zeke came face to face with the Slender Man. Zeke, paralyzed with fear, stood staring directly into the blank face of the Thin White Duke. The Slender Man took this as an offensive gesture and impaled him upon a tree branch. Bleeding out at an alarming rate, Zeke began to cry. He screamed for Jack to help him, screamed for anyone... But he received no answer. Finally, seconds before he faded into unconsciousness, Zeke saw his saviour; The Blind Man.
When he awoke, he saw a hooded figure standing at the foot of his bed. Standing next to him was the most beautiful woman he had ever seen. The two entities revealed themselves to be Deimos and Diesis, the Extension Fears of the Unnamed Child and Blind Man respectively. They then informed him that he had been in a coma for over a month... And told him what had happened to his family as a result. Saddened, Zeke asked what he could possibly do now. Diesis responded by telling him that she would gladly welcome him into her "Knights of the Eternal" and treat him as though he were her own son. He immediately accepted.
Being a mere ten years old, Zeke was assigned to simple jobs such as deliveries and danger-free infiltrations. Amused by his personality, Deimos nicknamed him "Phobos" and began to treat him like a younger brother. And then came the day that Diesis and Deimos forged an alliance with one another. This led to Deimos' few willing followers being integrated into the ranks of the Knights of the Eternal. One such follower was Abel Parker, who would soon grow to be Zeke's greatest friend and ally.
Life serving the Extension Fears continued as normal for seven years, until Diesis began to hear rumors of an ex-proxy gathering an army to fight his master with.
Curious, she sent in Zeke to infiltrate and observe.
And observe he did. The alleged ex-proxy, who went by the name of Nathan Umbra, inspired Zeke. He seemed to show that even if one lived a terrible life under a Fear, they could redeem themselves. They could become a hero.
Or so it seemed.
The night before Zeke was going to return to Diesis, Nathan enacted his final solution. Gathering the hundreds of followers he had gained, he had his master force them all into the Path of Black Leaves. All but one.
It was at this point that Nathan showed his true colors. The person who had looked up to him... Idolized him... He had tied to a concrete slab and tortured for weeks. Zeke had opened himself up emotionally, and Nathan used this fact to break him. He built Zeke up, if only to knock him down that much harder. Even harder on Zeke's mind was that Diesis never attempted rescue, furthering his sense of hopelessness. Finally, on Christmas Eve, Zeke managed to break his restraints and escape.
But not before Nathan tortured the location of Diesis' mansion out of him.