Neither party is contesting that the documents were stolen [1]. Everyone is basically assuming that he did it; Uber's defense in this preliminary-injunction hearing is that the stolen documents never made it to Uber.
Uber wants to have its cake and eat it too. It wants to not be stopped by an injunction from Waymo, but it also wants to keep Levandowski as the head of its self-driving car program. Probably those two desires are in conflict; probably Waymo will push in the right places to force them to be in conflict.
If they can do that, it would change from Uber vs Waymo/Alphabet to Levandowski vs Waymo/Alphabet and Levandowski vs Uber.
If I was Uber, I know which fight I'd want to step into.