Shredder decided that once he got rid of the poison, he would immediately go into hiding.
Tokyo had a lot of sewer pipes; more than that, there were plenty of blind spots that no one else but Shredder in his blood form could reach.
After a few days, the Blood God Experimental would return to normal, and he would slip into the ocean.
Nobody would be able to find him then.
How had Shredder survived all this time? Because he was cautious (a coward).
His adopted son, Sacks, and his adopted daughter, Karai, were dead. His accomplice, Garrett the Clairvoyant, was dead. In the last few months, a lot of Hydra executives had also died.
Shredder was still living very well.
In this world, the last to remain was king.
After a few days, he would be able to go back and seize control of the Japanese branch.
Once Hydra was back in action, he definitely didn't mind having another capable helper.