The best science fiction explores ideas rather than just explosions and predictable third-act twists, a difficult challenge considering that most audiences apparently hunger for more of the latter. The new sci-fi thriller “Source Code” succeeds both as a well-crafted thriller and a philosophical exploration into free will/the nature of reality. These theoretical issues are imminently important to the difficulties of the plot.

Jake Gyllenhaal plays Coulter Stevens, a helicopter pilot whose last memory is of his copter being shot down; he then awakens on a Chicago commuter train, being spoken to by a beautiful woman (Michelle Monaghan) who claims to know him by a different name. Before Stevens can satisfactorily make sense of things, the train goes kablooey, and he finds himself in some kind of capsule, being questioned by Colleen Goodwin (a terrific Vera Farmiga).

Goodwin explains that he is a part of a government program called source code that allows him to relieve the last eight minutes of someone’s life, and that he must identify the train’s bomber to prevent a second nuclear attack on Chicago. Stakes sufficiently raised, he must go back to the train over and over, though Goodwin sends him back without answering his questions.

A ridiculous sounding premise, I know (difficult to explain, too). Even so, the movie is so well made that you hardly notice. Director Duncan Jones, who previously made the wonderfully weird “Moon”, balances the tender moments of last-day-on-earth romantic boldness with Stevens’ complete lack of information.

In fact, the director restricts what we as the audience know to what Stevens knows, allowing us to feel and relate to his surprise and confusion without in turn confusing us. This narrative move is particularly effective because, even though the movie has a traditional studio ending (Spoiler alert: He gets the girl!), the lack of information allows for actual, surprising twists in the midst of Hollywood formula.

And make no mistake, “Source Code” certainly adheres to the basics of a formula, albeit one with more inspiration from the great “Groundhog Day” than from turgid fare like “Transformers: Revenge of the Fallen”. The goal-oriented protagonist does manage to (surprise!) accomplish his goal, prevent disaster, resolve unresolved emotional turmoil, meaningfully change from turmoil and share a (literally) time-stopping kiss just in time for tea. That said, though, Jones (with help from a terrific script by Ben Ripley) tweaks the formula enough to actually overcome some of its flaws.

A good example of Jones’ subtle subversion of the Hollywood thriller genre can be seen with the film’s handling of its terrorist villain. Most wannabe blockbusters invest tremendous importance in their villain, crafting elaborate back-stories to explain their motives (evil rarely just is anymore), but “Source Code” will have none of that. Instead, the movie focuses in on Stevens’s quest for the villain’s identity.

When answers are not easily forthcoming, Stevens’s questions to Goodwin about the nature of the capsule he appears to be trapped in and source code itself become existential rather than simply practical.

When Stevens does track down the bomber (Michael Arden), there is no drawn-out explanation of motives, simply a short, appropriately crazy declaration (something about creating rubble from which humanity will rebuild itself).

In the trite-est of the trite, movie villains are very stale, figureheads of stunted evil whose fate is inevitable defeat at the hands of the righteous hero. Though Stevens does manage to prevent the nuclear attack by uncovering the name of the bomber, the repeatable nature of the premise means that the movie does not dwell overmuch on the stopping of the villain, which in turn avoids cliché.

Once the villain is stopped, however, the movie does not end: his plot itself was only a sideshow for Stevens’s dilemma, one involving his inability to save everyone on the train, including himself. I don’t want to give too much away, but the last 15 minutes of the movie feel like studio notes of some kind, trying to let Stevens have it all.

In the end, though, the cleverly-crafted narrative of “Source Code” has much less to do with saving the world than with Gyllenhaal’s well-acted existential confusion over the nature of his choices. In fact, all the acting in this movie is tremendously good, especially the chemistry between the two leads. Though the end of the movie feels like a combination of both homogenous studio notes and open-ended multiplane mind-bender, the movie itself is very much worth seeing.