Was Rex's mutiny against McCullen simply the seizing of an opportunity, or had it been part of the plan all along? Rex already had a special nanomite solution prepared for McCullen, as well as his own sub already branded with the Cobra insignia. It's worth noting that, in the sequel, both Zartan and Storm Shadow, who were previously loyal to McCullen, serve Cobra Commander without explanation, and nobody seems to have a problem when Cobra Commander abandons Destro, implying that Rex had quietly secured the allegiance of McCullen's lieutenants, and had been planning to hijack his Take Over the World plan all along.
When Zartan destroys the mind control chip during his surgery, McCullen looks concerned for a moment, while the Doctor doesn't even blink. Was this just Zartan being savvy and the Doctor not caring, or a sign that Zartan is already loyal to the future Cobra Commander? Either way, guess who's Cobra Commander's Dragon in the sequel.
With the Korean Byung-hun Lee playing the normally Japanese Storm Shadow, coupled with him speaking Korean in his youth, leads to the theory that Storm Shadow underwent a Race Lift in this continuity. Interestingly enough it would be another connection to his rival Snake Eyes as both are outsiders to the martial art they practice.
Cliché Storm: The film is chock-full of every action movie cliche most people have ever seen. If you want an explanation, look no further than Christopher Orr's review of the movie, in which he decides to just let it speak for itself by providing 40 of the lines that sum up the plot and all of the typical one-liners and plot points it has. It's really a shame though, considering it had some great actors who did the best they could with the material they were given. Then again, for fans of the movie, this could be exactly what they liked about it.
The Doctor/Cobra Commander is the Diabolical Mastermind behind Cobra, and the ultimate villain of the films. Once a soldier named Rex Lewis who was left to die by his military allies, the Commander embraced his abandonment, as it gave him time to weaponize the nanomite technology and ally with James "Destro" McCullen of MARS Industries as "the Doctor". Using the nanomite technology to mind control a variety of soldiers—even his own sister Ana, the future Baroness—"the Doctor" planned to assist McCullen in using the nanomites to wipe out major cities, before using Zartan to replace the President of the United States for ultimate power. After the nanomite plan fails, "the Doctor" betrays McCullen, uses Ana as a hostage, tries to blow up his entire lair and everyone inside and christens himself Cobra Commander. Later escaping prison, the Commander uses Zeus to destroy London, promising to continue wiping out entire cities until the world cows to Cobra.
Zartan is the Commander's right-hand psychopath, a Master of Disguise whose sadism and cheerful personality make him far worse than any other servant of Cobra. His introductory scene showing him stabbing Cover Girl through the back and mocking her as she dies, Zartan assists in killing a variety of Joes before killing a man for his clothes to evade capture. After capturing and replacing the President of the United States, who he regularly tortures for information, Zartan orders the execution of the G.I. Joes and kickstarts a war in a foreign country to enable Cobra Commander's escape. At the demonstration of Zeus, Zartan giddily pulls the trigger that blows up the city of London, England, and is revealed to have been the one who killed Storm Shadow's master as a child and corrupted him into evil, cementing himself as the worst Cobra has to offer alongside its Commander.
Draco in Leather Pants: Storm Shadow is very popular. Doesn't hurt that he's hot and can kick your ass from here to next Tuesday.
Fashion-Victim Villain: Cobra Commander. After switching to the metal full-head helmet, suddenly his skinniness becomes more apparent and he looks like a bobblehead or lollipop. One of the few cases where Shoulders of Doom might help.
Christopher Eccleston's character designed the bunker under the White House. Did you know that as The Doctor he operated the bunker-like office in 10 Downing Street (the Prime Minister's place)?
Snake Eyes is a ninja trained in martial arts. Young Snake Eyes was played by Leo Howard. Leo Howard and martial arts? That sounds familiar...
HSQ: Snake-Eyes is so awesome that Storm Shadow has developed an innate "Snake-Eyes just did something awesome" sense.
Magnificent Bastard: Cobra Commander, once known as Rex Lewis, was a soldier in the US military who was left to die, and takes the opportunity to go into hiding and perfect the nanite technology. Going undercover as "the Doctor", the Commander fools James McCullen into being his pawn, using the man's resources to secretly build his own organization called Cobra that the Commander uses to overthrow McCullen. Able to instantly silence any of his captured soldiers and even quickly using his sister Ana as a hostage to enable his escape from the G.I. Joes, the Commander installs Zartan as the President of the United States and uses him to eliminate the G.I. Joes and wipe out every country's nuclear weapons, at which point the Commander unveils his powerful Kill Sat Zeus, with which he hopes to gain ultimate power over the world, and very nearly succeeds. Cobra Commander escapes at the end of the films with many of his resources intact, and showcases a tremendous amount of manipulation and scheming in his quest to bring the entire planet under a Cobra banner.
Moral Event Horizon: The Doctor crosses it when it's revealed that he brainwashed his own sister (who, it should be mentioned, is in mourning because he allowed her to think that he was dead), and is ready to kill her to save himself and spite Duke. While he was already a sadistic Mad Scientist helping in a plot for world domination, this revelation puts him over the line from bad to pure evil.
Narm: Cobra Commander does a grand entrance... and is caught and put to jail few seconds later.
Most, if not all of the dialogue from the Doctor (no, notthat one) is incredibly hammy, but Joseph Gordon-Levitt makes every single bit of it work. The crowning moment has to be when he declares himself Cobra Commander. Could have been very ridiculous (especially with that look), but it manages to be a Moment of Awesome.
The Doctor: The time has come for the Cobra to rise up and reveal himself. You will call me... Commander!
The entire movie is blocked with cliché's, and is burdened with a fairly thin plot and an overabundance of special effects, but despite or even because of that, it's extremely entertaining.
Older Than They Think: The movie pulls ideas from several different toy lines, comic books, and animated series. Many of the details that fans complain about the movie "changing" are taken right from the source material ... just not an iteration of the source material the complainer is familiar with (e.g., you don't have to like the powered suits, but if you know the G.I. Joe: Sigma 6 line, you know the movie didn't make them up).
Likewise "International Heroes" was part of the Action Force theme, and even briefly adopted in the DiC series. GI Joe also worked for the United Nations in Sigma Six.
Doesn't help that they come off of as more of a Battle Couple than Scarlett and Snake-Eyes, the ORIGINAL pair of leading lady and badass ninja.
The novelization seems to add considerable mutual witty banter and, yes, flirtation and, it also offers Ho Yay for Snake Eyes and Storm Shadow, who seem to be matching Official Couple (sort-of) Duke and Ana/The Baroness flashback for flashback, meaningful look for meaningful look. (Bizarrely carries over to the Ninja Showdown kid's book.) Oddly out-of-place due to the gist of their past relationship being "We really, really don't like each other."
Romantic Plot Tumor: The Baroness and Duke is pretty central to the storyline, even if it feels unnecessary to the mythos. G.I. Joe, after all, has no small shortage of improbable relationships across every canon. Ripcord and Scarlet, however, seems to have drawn almost universal scorn.
Special Effects Failure: While a majority of the special visual effects were well done, a CGI cobra at the beginning of the film sticks out like a sore thumb.
They Wasted a Perfectly Good Character: Cover Girl in this movie is basically just General Hawk's assistant before Zartan kills her. Cover Girl in the source material is a former professional model who took up driving tanks for a living. Not even the G.I. Joe fans realized that the character was supposed to be Cover Girl. You know you've wasted a character when not even the people with knowledge of the source material knew who the character was supposed to be.
WTH, Casting Agency?: You'd never imagine Marlon Wayans and specially Joseph Gordon-Levitt in this movie. Surprisingly, Joseph Gordon-Levitt really pulls it off, and Marlon Wayans... is, well, Marlon Wayans, although even he tones down his fundamental Marlon Wayans-ness a bit.
Channing Tatum as the leader of the Joes? Seriously?
Snake Eyes' mask having embossed lips. The idea of a character who doesn't speak having embossed lips on his mask is just ridiculous. It also proved distracting to the audience.
Rex's "Cobra Commander" helmet. Whoever was in charge of costuming either had no idea what the Commander looked like besides "shiny helmet", or tried to somehow combine Rex's look before he revealed his true colors with the look commonly associated with CC. The result◊ was...interesting.