So, let me see if I've got this straight... April's dad was working with Shredder (who appears to be white, so I'm guessing his real name isn't Oroku Saki in this film...) to "create heroes," and it's implied that they created the mutagen that mutated the turtles.
So extrapolating on what we know: April's dad was a scientist working for the Shredder, but the Shredder turned out to be evil wanted to use April's dad's work for his own evil ends (you know, as opposed to all the humanitarian ways you can use a mutagenic ooze). Shredder then had her dad killed - probably for stealing the ooze and hiding/trying to destroy it, which of course is where the turtles came from.
When the turtles appear, Shredder takes notice and wants to capture them so he can experiment on them and create more mutants which he can then use in his plan for world domination. April and the turtles team up to take down his evil empire.
Did I miss anything?
Oh yeah, the joke at the end with Michelangelo was pretty funny.
I may watch this when it comes out on DVD. But I'm not sure. The turtles were my first superhero love. I was a huge Ninja Turtles nut as a kid, I don't know if I can handle watching Michael Bay's interpretation.