Superhero films based on existing material have a hard road ahead of them at this point. With critical acclaim for a wide variety of stand alone stories (like The Avengers, Thor, and Captain America: The First Avenger), the writers of future superhero films have to balance the line between the well-read fans of the franchise and the new fans who only know the characters and worlds from the films. New concepts need to be introduced to keep the stories going, but they need to be explained in such a way that they make sense to the lay person and don't bore the experienced fan. Iron Man 3 sees Tony Stark dealing with the repercussions of The Avengers. He can't sleep, he's obsessed with improving the Iron Man suit, and he's starting to have anxiety attacks. Pepper Potts is totally over his work obsession and has her own issues running Stark Enterprises, where scientist Aldrich Killian pitches a partnership over the ability of the brain to regenerate and reshape the body however you want. And then The Mandarin announces himself to the world as a terrorist punishing America for its crimes with mysterious bomb-less explosions.
If the plot summary doesn't make it clear, screenwriter Drew Pearce and writer/director Shane Black put a lot of story in Iron Man 3. Arguably, they put too much story in the film. The plot points are not balanced at all and the main thrust of the story, the mystery of The Mandarin's terrorist attacks, is severely under developed. If you're not familiar with the briefly mentioned but never explained Extremis, you might get lost.
The Extremis really is the cause of and solution to all the structural problems in the film. It is not the most well-known aspect of the Marvel universe. It was created for a limited-run six issue comic in 2005 and adapted for one episode of an animated Iron Man series. The Extremis is mentioned a handful of times in the film but no one ever says what, exactly, it is. They beat around the issue--bioengineering, injections, regenerative properties--but never really introduce it. That's a problem.
To tie into The Avengers, Tony Stark is haunted by the battle in NYC. He also begins to write and see signs of Thanos everywhere he goes. Without a definite explanation of the Extremis or Thanos in the film, it starts to get muddled. Until I realized that the Thanos visions were totally unrelated to the main plot of the film, I thought the Extremis was some alien technology that got out of hand.
It would not have been hard to have included 20 seconds of exposition about the Extremis the same way that Iron Man 2 concisely explained how Ivan Vanko harnessed the arc reactor to make a weapon or even how Iron Man explained the arc reactor. You can have all the plot in the world and still be a total mess if you skip out on necessary exposition.
The mishandling of the Extremis is a shame because Iron Man 3 looks and plays great. The cast is on top of these roles. The introduction of new suit features and designs is explained perfectly. The visual representation of the Extremis is unnerving in the best way possible. The reveal of information in the final act is simultaneously hilarious and believable.
Best of all is the choice to explore the relationship between Tony Stark and Iron Man. In the second film, the two become synonymous and continue that way through The Avengers. Now, it's a source of fear and anxiety for Tony Stark. From the beginning of the film, he only feels safe if he's constantly working on or inhabiting the suit. Anytime he's forced to step away is a much-needed break from the fantasy of fame in Iron Man and an actual justification for continuing the series.
If the screenplay were just a little clearer, Iron Man 3 could arguably be the best of the Marvel superhero films. The screenplay is just too muddy and ill-defined to even be considered good. The film is enjoyable despite the poor writing, though it comes close to sinking the whole thing.
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