Presence in the City
Approximately an hour later, Rex retrieved the crystal when the Jar of Malice's interior began to show signs of glow with vibrant intensity, deeming it sufficient. Despite not being fully fueled, he decided to heed the Witch's warning.
It's true that the Witch wanted to kill him, but he reckoned that she would not try it now.
Doing it now would be foolish of her.
Rex knows that the Executor knows too much about her due to coming from the past and that in itself was a threat to her. Her plan, if she has already devised one, is to use him to take down the Executor first before making her move.
Oblivious to her, Rex saw right through and is already aware of her scheme.
Most of the past enemies that he already defeated made the mistake of triggering a quest from the System, which he was forced to complete. But it was not their fault, the System is completely unknown by anyone.