Eli was high above in the New York Sky's in desperate search of a being known to the world as Scorn. He knew with not a doubt that when he found the rouge sand conduit, he would find scorn.

He was later proven to be right when he was a witness to what basically amounted to murder. CTU never stood a chance against her, it wasnt much different than putting a gun to their head pulling the trigger. 

He thought he saw someone with her but he was too fixated on her to worry about anyone else. Thoughts ran through his mind if he should save the innocent people down there who were too stupid to run when they had the chance. He also knew that any fight they would get into wold only kill more people and cause more destruction. He stayed in the air, angery and watching the goings on down below.