"Star Trek Into Darkness" has all of the components to be an awesome summer movie spectacular. It has J.J. Abrams, the energetic blockbuster director who revived the franchise back in 2009 and had one of the best summer movies just two years ago with "Super 8." The spirited cast hasn’t lost any of its fun liveliness since the first installment, and the special effects-driven action is still as breathtakingly intense as it is breathtakingly gorgeous.

With all of that in place, it would seem the sequel’s phasers would be all set to stun. But something’s off. There’s a sequence where the starship Enterprise is flying at warp speed when a big, clunky-looking vessel comes up from behind and nudges it off its exhilarating track. That’s pretty much "Star Trek Into Darkness" in a nutshell, except replace the big, clumsy vessel with a big, clumsy story.

Captain, I detect spoilers throughout the rest of this review.

After breaking the Prime Directive on a fun, frenzied and emotionally full-gear opening mission, Captain Kirk (Chris Pine) and Spock (Zachary Quinto) arrive back home to demotions. Their punishments are short-lived, however, as a Starfleet agent-turned-terrorist named John Harrison (Benedict Cumberbatch) attacks his former organization, killing Kirk’s captain and fatherly mentor (Bruce Greenwood) in the process.

The attacks leave Kirk and the rest of Starfleet hungry for revenge. They track Harrison to a planet deep inside Klingon territory, causing the head of Starfleet ("RoboCop" star and Stevens Point native Peter Weller) to send Kirk and company off to bring Harrison to brutal justice. However, hastily barging into Klingon territory would almost certainly ignite a war between the two tense intergalactic rivals. If this sounds vaguely similar to 9/11 and the War in Iraq, the pre-end credit dedication to post-9/11 war veterans would seem to confirm that the bizarre allegory is no accident.

While Kirk’s original orders were to carpet bomb Harrison’s location from a safe distance with some experimental missiles (drones were also apparently on the screenwriters’ minds), Kirk instead decides to take the terrorist alive and bring him back for courtroom justice. Harrison then unveils Hollywood’s worst kept secret: Yup, he’s actually Khan, a 300-year-old super soldier with a bone to pick with Starfleet. A web of backstabbings, mind games and bad decisions begins to unfold.

Unfortunately, the trio of writers – Damon Lindelof, the man behind "Prometheus" and much of "Lost," alongside Roberto Orci and Alex Kurtzman – have the same care and consideration for storytelling that Khan has for his enemies’ skulls. Take the first act, where the movie focuses on Kirk’s demotion down to first officer, only to put him back in the captain’s chair maybe 15 minutes later. It’s treading water disguised as plot movement.

The film’s habit of continually tying itself into tedious knots only gets worse as the overly convoluted conspiracy takes center stage. Don’t let your brain’s strained attempts to comprehend the evil plot fool you: It’s dumber than a bag of space rocks. Any brainpower expended trying to piece it all together isn’t because "Star Trek Into Darkness" is outsmarting the audience but because the mind is foolishly attempting to make up for its gaps in logic (the stuff with the missiles and their secret cargo? Nonsense), muddled character motivations and the fact that none of its components quite gel into one coherent, compelling whole.

Even with all of the epic space battles and Enterprise crew members frantically running around everywhere, the movie can’t help but sag under the weight of its excessively complicated plot machinations.

In the end, all that conspiracy malarkey ends up useless because Khan is in this picture. Anyone with a passing interest in "Star Trek" knows you don’t bring back the franchise’s signature villain just have him play second fiddle to some random Starfleet war shenanigans. So the movie just becomes a predictable waiting game for the hyper-articulate Khan (seriously, Cumberbatch devours every syllable) to take over.

When he does in the last act, the film reveals its final form: It’s a rehash of "Star Trek II: The Wrath of Khan," minus the sci-fi classic’s originality and conviction. Call it fan bait. Call it merely a shadow of its predecessor. All would be correct, but I prefer half-committed. The uneasy fit between the Starfleet drama and Khan makes it feel like the movie wasn’t sure which storyline to go with, so they went with both.

I should probably stop taking a crowbar to the story, though there’s plenty more – like Alice Eve’s new character whose only purpose is to be in her bra for one scene because it’s a summer action movie, and they know where their money is coming from this weekend – that deserves a firm verbal smack.

As I said early on, there are a lot of things I like about "Star Trek Into Darkness." Chris Pine makes for a charming Kirk, Quinto brings a lot of humor and complexity to Spock and the always entertaining Simon Pegg makes the most out of his expanded role as Scotty the engineer. When the script doesn’t have to explain the baffling plot developments, it’s actually quite sharp and funny, and Michael Giacchino’s score is still suitably grand and epic.

There are some spectacular action sequences too, including a breathless, spaceship-free trip through a debris field and a scene involving a freefalling Enterprise that sends the crew running and sliding up the walls (been watching "Inception" a bit, Mr. Abrams?). Even the 3-D is above average. It’s just too bad during many of these moments, instead of marveling at the spectacle of it all, I was still stuck a few scenes back, trying to untangle a messy plot point or figure out a character’s seemingly mindless motivations.

"Star Trek Into Darkness" is still an entertaining trip, just also one that’s, in the words of our pointy-eared friend, highly illogical.