The "hooded man" was actually the disguise of an old woman, Mrs. Baker, a counterfeiter.
It's easy to tell that it is Mrs. Baker because the costume looks almost identical to her regular outfit, featuring a pink robe similar to the dress she normally wears and the same purple cloak. The hood is purple on the back and black on the front, and it makes her eyes appear large and green.
The hooded man was sneaky and sinister. His actions at the auto-junkyard showed that he wasn't above killing.
Skills and abilities
The New Scooby-Doo Movies
While Batman, Robin, and the gang were investigating an auto-junkyard looking for counterfeiters, Shaggy Rogers and Scooby-Doo saw the hooded man sneaking around. They got scared and hid in an old wreck. The hooded man proceeded to man the crane and attempted to lower the two into a car crusher. They were rescued by Batman, who hooked the wreck with his batline so they could slide down and get out of the wreck before it was crushed.
The hooded man was discovered again after the mystery of Mrs. Baker's disappearing farmhouse was solved; it rotated underground and was controlled by a hidden lever. He was chased into a secret warehouse filled with huge toys. He threw a giant bouncing ball at the gang, and much running around ensued. Scooby ended up riding on a runaway toy car and started crashing into numerous toys. He eventually hit the crate the hooded man was hiding in, flushing him out. Robin tried to capture him, but Scooby's car crashed into the jack-in-the-box he was standing on, causing it to spring open. The hooded man hid in a teepee, which Shaggy stumbled into after a huge elephant mask fell on his head. The two ran around in the teepee for a bit, then fled in different directions. The hooded man got on a unicycle and attempted to make a getaway. Fred Jones, Daphne Blake, and Velma Dinkley spotted him, so they got on bicycles and chased him. He eluded them by riding under a volleyball net which was high enough for him and his unicycle but too low for the bikes.
Scooby, still riding on the runaway toy car, crashed into a sandbox, causing him to fly out of the car and onto a seesaw while the hooded man was riding over it, flinging him into the air. The hooded man fell through a basketball hoop where Batman and Robin were waiting to catch him. Before the unmasking, the gang asked "him" what happened to Mrs. Baker, only to discover that the culprit was Mrs. Baker herself.