It had already completed its top secret mission and had stopped in Guam after Tinian to exchange some crew. Why was the decision made to have it go alone from Guam to Leyte without any escort ships? If it had had an escort accompanying it, they could've aided in rescuing much of the USS Indianapolis crew after the sinking, especially since about 50% of the USS Indianapolis' crew died only after being set adrift due to a number of factors like exposure, dehydration, starvation, and shark attacks. Wasn't it standard procedure in the navy by this point in the war to not let capital ships travel on their own?
You may find this Ask Historians thread to be helpful especially the comments of /u/white_light-king