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In all the movie's promotional materials, the only reference to Joseph Gordon-Levitt's portrayal of the character was snuck into the background of a single poster. Even the film's trailers didn't tease us with any glimpses of Cobra's evil leader.
At first I thought they might be keeping him hidden for a big dramatic reveal. But thinking back to Heath Ledger's Joker in The Dark Knight as a counter-example, why would producers who are desperate to build buzz and sell a movie keep something cool under wraps...? Well, because that something actually sucks.
Then a rumor emerged that director Stephen Sommers was fired from the film during post-production. That has since been denied, but either way, it speaks to problems on the set/in the lab.
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It seems the filmmakers (whoever they were) swapped out his vocal performance for an anonymous and uncredited voice actor.
And unlike David Prowse's voice being replaced by James Earl Jones in the Star Wars films, this swap seems to have been unplanned. Consider these comments from Gordon-Levitt before the film wrapped:
"I love that voice [from the cartoon]," enthused Gordon-Levitt. "Chris Latta [the original Cobra Commander] is a fantastic voiceover artist, but if you did that exact voice it would sound ridiculous in a live-action movie. I guess it's half Chris Latta and half me."Turns out the his half-and-half vocal take didn't impress. Because if this isn't another actor, then there's some serious auto-tuning going on:
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