TLDR: As a kid, I always thought Donatello was the black Turtle.
I have a feeling the tall shadowy figure is a Utrom (Captured from Roswell? Wouldn't put it past them) in a humanoid suit, and William Fichtner's character is "The Shredder" character. Actually, as an AU, this doesn't sound like a bad idea...
Utrom ship crashes. Mr. Shredder manages to harvest the technology and capture a live alien from which to grow a major tech company, of which Mr. Oneill, a rising star in computer/electrical/biological engineering, becomes an employee. He's assigned to study a chemical formula that has mutational properties, when his initial results reveals Shred's plans to use the substance to develop a mutant super-soldier program. Mortified, Mr. O steals what remains of the substance and makes a harrowing escape, dying at the hands of Shred's goons but not before the substance can get tossed down the sewers.
15 years later, Shred's using his covert connections to the Foot terrorist organization to guarantee huge subsidies from the DOD, when his plans are thwarted by what he eventually realizes is the product of the long lost mutagen. Hoping to study and use the creatures as a prototype platform to reproduce the material, he captures three of the Turtles. Raphael rescues a weakened Splinter and the two kick off a hit and rescue operation at one of Shred's remote labs. The mini-war for the mutagen escalates when Shred uses Utrom tech to create an Iron Man-esque battle suit to take down the Turtles once and for all.