Star Trek Enterprise and Terrorism
By the end of season two, Star Trek producers decided to tackle 9/11 head on. In that season's final episode, a probe from an unknown alien source unleashes a devastating assault on Earth killing millions, including Trip's younger sister. After Captain Archer learns that the probe that attacked Earth was sent by the Xindi, a distant species who believes humans will destroy their home world in the future, he and the crew decide to go find the Xindi in a mysterious region called the Delphic Expanse in order to stop them from developing a more powerful weapon that threatens to destroy Earth. The epsisode The Expanse marked the beginning of year-long story arc that would focus on the Enterprises efforts to thwart any future Xindi attack. http://www.youtube.com/watch?v=6QzCFcXUh0E The Xindi storyline was clearly informed by 9/11, when alien terrorists staged an unprovoked attack on the United States, producing much death and devastation. Trip and Archer mirror the desire for vengeance that dominated the American landscape in the wake of the attacks. In some ways channeling the views of the Bush Administration, Trip observes that he hopes that the Enterprise crew will not be stopped by that non-interference crap T'Pol's always shoving down our throats. Archer agrees that they will do whatever it takes to spare Earth from annihilation by the Xindi. The Xindi attack and the crews reaction were not the only parallels to post-9/11 terrorism. Rather than have Enterprise remain near Earth to protect it, Archer instead takes the battle to the Xindi homeland, just as the United States government took the war to Afghanistan in its global war on terrorism. The depiction of the Xindi homeland the Delphic Expanse in many ways mirrored descriptions of Afghanistan as a mysterious and dangerous region home to hostile ethnic groups, and where powerful groups, like the British and the Soviet Union, seemed to have lost their way and struggled to survive. The Xindi themselves, comprised of several different species, including insectoids, reptilians, and aquatics, seem to resemble the fractured Afghan society dominated by numerous powerful warlords. 
While the Xindi arc was informed by the 9/11 attacks and subsequent war in Afghanistan, the numerous episodes that make up the arc don't really explore the issue of terrorism. In a season three episode Star Trek producers tackled the relationship between terrorism and religious extremism. Like "Desert Crossing," in "Chosen Realm" the Enterprise crew comes to the aid of a crippled alien vessel. Befriending these aliens who call themselves the Triannons, Archer learns that they are a deeply religious people who consider mysterious spheres the Enterprise discovered while in the Delphic Expanse as sacred objects. Claiming that Enterprise has desecrated these sacred spheres, the Triannon sieze control of the ship by threatening to blow up the warp core using suicide bombers. The Triannon leader D'Jamat wants to use the Enterprise to defeat a rival sect on his home world who he claims are heretics. Before he can engage in this war against heresy, Archer and his crew are able to regain control of the ship. The final scene has Archer taking the captured Triannon to their planet where they discovered that the battle between the two religious sects has completely destroyed the Triannon home world. http://www.youtube.com/watch?v=jPzqnzh_3Lo&feature=related Part 3 is below...