Spoilers ahead.
The two first forays into the 2013 "summer" movie season, Iron Man III and Star Trek: Into Darkness may be the first of several films this year to feature villains who remind viewers that the sins of our past will always come back to haunt us.
In Iron Man III the film's major villain, Aldrich Killian (Guy Pearce), was slighted twenty three years ago by the self-absorbed, rich whiz kid Tony Stark (Robert Downey Jr). Killian masks his revenge against Stark with The Mandarin (Ben Kingsley) and a series of apparent terrorist attacks. Behind all the theatricality lay a simple tale of a man who was humiliated and wants his just desserts. Stark works to unravel the mystery of The Mandarin and Killian while saving everyone around him, including the President of the United States. More than Stark, however, it's his friend James Rhodes (Don Cheadle) who frequently has to question his allegiance. As "The Iron Patriot" (formerly "War Machine" -- a very telling change) he's done up in a garish red, white and blue suit. Throughout the film there's a recurring question as to who is really in the suit and what their motives are.
Similarly, in Star Trek: Into Darkness there are two villains: Admiral Marcus (Peter Weller) and Khan (Benedict Cumberbatch). Like The Mandarin, Khan serves Marcus (and with about the same amount of loyalty) as a pawn in a larger end game. Unlike The Mandarin, the threat of Khan is far more than what is initially promised. He's not just some random terrorist who saves a little girl in order to destroy a secret weapons lab. He is everything that The Mandarin might have been.
Khan led a crew of 72 genetically-modified men and women in the Earth's past. They were convicted of war crimes and exiled from Earth. Marcus uses the discovery of their derelict ship to his advantage by taking Khan out of cryo-sleep and employ's Khan's superior intellect and ruthlessness to create newer, better weapons. That's the stated reason, anyway. The audience never sees these weapons and why someone 300+ years old can come up with more advanced weapons seems to be a ruse. What Marcus really wants is a walking powderkeg to ignite a war with the Klingon empire.
Into this rather elaborate set-up steps James T. Kirk (Chris Pine) who needs to learn a lesson in humility and teach a lesson of friendship to Spock (Zachary Quinto). Much of Star Trek: Into Darkness bounces Kirk between lies as he tries to discern the truth of his situation. He's sent to kill Khan (who's using the alias John Harrison) "with extreme prejudice." Kirk wants revenge for the death of his mentor, Captain Pike (Bruce Greenwood) and Marcus arms him with weapons of mass destruction, 72 modified photon torpedoes. Marcus also provides Kirk with permission to go on a rogue mission to Kronos, the Klingon home world. There, Kirk is supposed to strike without warning in an attack that sounds a lot like a drone strike.
Both Iron Man III and Star Trek: Into Darkness attempt to explain terrorism and the hatred certain groups and people feel against the United States. Kirk and Stark share an arrogance that is dwarfed when compared to the overreaching dogmatism of what they represent: Kirk the Federation and Stark the United States.
The Federation is so cavalier that its offices are in high buildings with plenty of windows. No one would attack their headquarters. Not only does Khan attack it directly but he also attempts to lay the entire city of San Francisco to waste by crashing a starship into it. Of course, this is the moment where 9/11 metaphor should crystallize for every viewer.
Khan attacks three times on Earth. The third mirrors 9/11 while the first recalls the 2005 London bombings. It's the second that sets Kirk on his path of vengeance. It's his "now it's personal moment."
Kirk quotes Kautilya's "The enemy of my enemy is my friend" about Khan. This phrase was adopted too readily in U.S. foreign policy. Wars fought by the United States in the last two decades include former "friends" such as Iraq and Afghanistan. Like the American people, Kirk is duped into going into battle with an enemy while blinded by vengeance and sold a story by a madman. Just like past dirty dealings, the allegiance with Khan goes totally wrong.
Of course, everything is set seemingly correct by the end of each film though at what cost? Pepper Potts (Gwyneth Paltrow) has been exposed to a terrible virus that threatens to consume her in Iron Man III while war with Klingon is still imminent in Star Trek: Into Darkness.
What will our next lesson about the past coming back to bite us in the ass be? It seems most natural that Man of Steel will fulfill this promise. General Zod embodies "the sins of the father" revisited upon the son.