As we sailed through Y2K and nothing really happened, the 2000s arrived, and cinema underwent a radical shift. Science fiction films of the decade tackled new concerns about growing technology, and thanks to advancements in VFX, it was easier than ever to bring high-concept films in on a cheaper budget. Sci-fi films in the 2000s had a different flavor to them than in decades prior.

Updated July 28, 2023: If you enjoy watching underrated sci-fi gems from the 2000s, you'll be happy to know this article has been updated with additional content by Darren Gigool.

The decade saw a rise in superhero franchises like X-Men and Spider-Man, as well as two Matrix sequels, Transformers, and Spielberg going big with the genre again. Yet there were some smaller films that flew under the radar, either because of a limited release or were beaten out by other films but found new life on home video. These are the most underrated sci-fi films of the 2000s.

16 Cargo (2009)

Martin Rapold and Anna Katharina Schwabroh in Cargo (2009)
Atlantis Pictures

Intriguing and chilling, Cargo serves as a profound commentary on the potential environmental calamity. This Swiss-made sci-fi, helmed by Ivan Engler and Ralph Etter, unfolds in 2267, an era where Earth's habitability has ceased. Life for humanity's fragments happens within space stations, which are congested and desperate. Dr. Laura Portmann embarks on a mission to Rhea, a remote planet, with a longing to see her sister again. As mysterious events unfold, the journey aboard the cargo ship Kassandra, once seen as a hopeful voyage, twists into an experience of inexplicable terror.

The rich thematic undercurrents and riveting storyline of Cargo have failed to secure the spotlight within mainstream sci-fi audiences. It boasts a complex narrative, top-tier production values, and an awe-inspiring representation of the cosmos. Its non-English origin, regrettably, might have hindered its reach to a wider audience. But for those science fiction connoisseurs in pursuit of uncharted territories, Cargo provides an immersive and deeply stimulating viewing experience.

15 Ikigami (2008)

A scene from Ikigami (2008)
Toho Company

In Tomoyuki Takimoto's Ikigami, it's all about the basic premise taking place in a dystopian future. The government has forced a program to be implemented among its citizens. When they reach a certain age, some of them will die. If you're picked in the lottery, you get a notice indicating that you have 24 hours to live.

Related: The Best South Korean Sci-Fi Movies, Ranked

The film is the portrayal of how three chosen ones live their last day on Earth, and it's a very good adaptation of the 2008 manga. It's dramatic under the standard of sci-fi, and it's a much more interesting film than audiences at the time thought.

14 Clockstoppers (2002)

A scene from Clockstoppers (2002)
Paramount Pictures

Clockstoppers is a Nickelodeon film. We won’t exactly deny that. However, it’s a solid entry in the catalog of sci-fi films made for younger audiences. It has a plot that’s only sustained because of how well its lack of logic plays into the tone of teen adventures. In this one, a teenager finds a machine that "speeds him up" while other people stand still. Of course, he uses it to his own advantage. Its special effects are among the best on this list, and it is a great follow-up to the bullet time concept introduced by The Matrix.

13 Possible Worlds (2000)

A scene from Possible Worlds (2000)
CBC / Mongrel Media 

Possible Worlds is an obscure movie that not many people were able to see. Even today, it's hard to find it online on streaming services. But if you do, don't miss out on the opportunity to watch a radically different sci-fi film.

It tells the story of two people meeting each other in two different instances as two different people. It sounds confusing at first, but there's a whole plot through which you'll be able to solve the riddle about a future experiment in which consciousness can be swapped between bodies. It features Tilda Swinton in an early but very good performance.

12 Pandorum (2009)

A scene from Pandorum (2009)
Icon Film Distribution

Considering the sci-fi standard, Pandorum complies heavily with the basic aspects of what makes the genre a perfect opportunity to explore hard-to-portray storylines. It’s violent, creepy, and organic in the sense of how its aesthetic combines well with the story. Performances are more than good and its story about the crew of a spaceship waking from hypersleep to discover everyone's missing is pretty interesting. For those who haven’t checked it out, you’re in for a treat full of twists. It has one of the best endings on the list.

11 The Cell (2000)

Vincent D'Onofrio in The Cell (2000)
New Line Cinema

Tarsem Singh made The Cell in 2000, and everyone accused him of casting Jennifer Lopez because supposedly she made the movie worse. Let us correct them: she's not bad at all in the film. It also stars the great Vincent D'Onofrio, and trust us when we say you have never watched a production design like this. It's unarguably the film's main character.

This is a sci-fi horror thriller in which we are able to explore minds through the use of intrusive virtual reality. It's very Inception-like, only the costumes are cooler. A child psychologist is forced to enter the mind of a comatose serial killer to find where he's hiding his latest victim. Again, we guarantee you will find yourself physically lost beyond the limits of a seriously corrupted mind.

10 Equilibrium (2002)

Christian Bale in Equilibrium (2002)
Miramax Films

Kurt Wimmer is a much better filmmaker than Hollywood says. His scripts are shrouded in logic and cleverness that’s hard to see in genre films. His Equilibrium is great proof of this. This is a future where feeling is illegal. Imagine the story arcs spawning from that, and starring familiar faces like Christian Bale, Emily Watson, Taye Diggs, and Sean Bean.

Sure, we mostly remember the special effects because they look great to this day, but Equilibrium is especially well-acted. We need to bring it back to modern audiences who see the future as a harmless and exploitable opportunity where the dangers shown by dystopian and apocalyptic films don't exist.

9 Reign of Fire (2002)

A scene from The Reign of Fire (2002)
Buena Vista Pictures Distribution

Rob Bowman's Reign of Fire is still a solid watch, even after all these years, that curiously gathered two great Hollywood talents before their prime in a genre film. Matthew McConaughey and Christian Bale star as the members of a dystopian society that somehow has managed to survive the reemergence of dragon creatures from the Earth. To end it all, they come up with a plan to exterminate the one creature that leads them all. Great visual effects and a peculiar over-the-top performance by McConaughey make it an early 2000s must-watch.

8 Slither (2006)

A scene from Slither (2006)
Universal Pictures
Mandate Pictures

Before dedicating himself to superhero films, James Gunn made films like Slither, and his world was infinitely more interesting. The horror sci-fi comedy features Elizabeth Banks and Nathan Fillion as residents of a town that gets invaded by a very slimy and sexy alien parasite. This one is reminiscent of mid-century B-movies that featured ridiculous creatures. It's a great debut for a young Gunn, who had only experimented from the writer's seat.

Related: These Are the Best James Gunn Movies (Plus Peacemaker), Ranked

Very well-produced special effects and a good dose of comedy accompany the sci-fi element that serves as a perfect backdrop for a unique modern film.

7 The Host (2006)

A scene from The Host (2006)
Showbox Entertainment

A potent fusion of traditional monster-movie elements and sharp political satire characterizes The Host. There's more to this film than the typical creature feature trope. Directed by Bong Joon-ho, this South Korean cinematic gem centers around a flawed family's rescue mission for their youngest, taken by a monstrous beast birthed from the Han River.

The shortage of broad acclaim contrasts with the film's standing as a hidden jewel in the sci-fi realm. The Host provides audiences with a refreshing angle on the monster movie genre, seamlessly integrating suspenseful sequences with a scathing commentary on South Korea's government ineptitude. For those who dare to venture into the deeper and dark aspects of this genre, The Host discloses itself as a distinct and layered addition to the sci-fi repertoire, deserving a watch.

6 Moon (2009)

Sam Rockwell in Moon (2009)
Sony Pictures Releasing International
Sony Pictures Classics

An innovative story circles Moon, with Sam Bell as the protagonist, portrayed by the multifaceted Sam Rockwell, approaching the final stretch of his solitary three-year tenure on a lunar base. Bell's journey takes an eerie turn as peculiar occurrences incite him to reassess his reality. Remarkably focusing on a lone person's life in space, Moon navigates the intricacies of seclusion with a delicate blend of creativity and profundity. If your quest is to find a sci-fi flick that captivates with grand space visuals and a narrative that demands cerebral engagement, this movie is a flawless pick.

More pertinent than ever in our tech-dominated present, Moon masterfully investigates themes of identity and solitude. Rockwell's portrayal of Sam, a man who has spent so much time in space, engrosses the viewers, pulling them into his sphere of doubt and isolation. The film's allure rests heavily on his riveting performance, infusing depth and suspense into the storyline. From his lonesome existence and mounting bewilderment, the film stirs the audience to ponder over their self-image and the psychological impacts of isolation.

5 Timecrimes (2007)

A version of Hector from the future in Timecrimes (2007) (Los cronocrímenes)
Karbo Vantas Entertainment

In Nacho Vigalondo's Timecrimes, time is of the essence. A man accidentally gets into a time machine and travels back in time only to find himself one hour ago and starts a series of dangerous, hilariously complex time loops. You will be confused before being able to say "paradox," but Vigalondo's Spanish film makes sense at some point. The tone is unlike anything we've seen in Hollywood before, but it works to make the movie more than just a time-travel adventure where the main character does things he shouldn't do. Constantly.

4 The Fountain (2006)

The Fountain (2006) by Darren Aronofsky
Warner Bros. Pictures

It's safe to say we all remember watching the trailer for Darren Aronofsky's The Fountain and being automatically interested even if we knew nothing about the film. It looked great, but most of all, it was unlike anything we had ever seen before, with mesmerizing visuals and cinematography that was sure to blow everyone's minds.

Related: Underrated Sci-Fi Movies of the '80s, Ranked

This one told the story of a scientist trying to find a cure for the cancer that slowly kills the woman he loves. But Aronofsky tells a story that's interwoven by two other timelines reflecting the same characters fighting against disturbances to remain in each other's arms. This is one romantic sci-fi film we will never forget, but it was sadly forgotten quickly by modern audiences who didn't quite connect with Aronofsky's motifs.

3 A Scanner Darkly (2006)

Keanu Reeves and Woody Harrelson in A Scanner Darkly (2006)
Warner Independent Pictures

Distinguished by its unique "interpolated rotoscoping" animation style, A Scanner Darkly presents an uncanny, dreamy aesthetic. Philip K. Dick's novel finds an authentic representation in the movie, echoing its nebulous and paranoid ambiance. The film proficiently delves into the issues of surveillance, addiction, and the essence of identity. Its depiction of a dystopian society, ever under the watchful eye and struggling with a drug crisis, pushes conventional limits and stirs up timely sociopolitical debates.

Yet, despite its revolutionary narrative approach and impressive visual expression, A Scanner Darkly lingers as an under-recognized masterpiece. The narrative's profoundness, paired with avant-garde animation, calls for broader applause, not merely from sci-fi enthusiasts but film aficionados across the board.

2 Sunshine (2007)

A scene from Sunshine (2007)
Fox Searchlight Pictures

A desperate quest to revive our dying Sun and rescue Earth from an impending ice age propels Sunshine. The narrative follows a space crew trying to accomplish this heroic feat. The storyline, brimming with colossal stakes, delivers an exhilarating voyage into space and survival.

Notorious for his genre-mixing mastery, Danny Boyle doesn't disappoint with Sunshine. In this cinematic spectacle, Boyle meshes elements of science fiction and horror, crafting a terrifyingly immersive tale that keeps audiences teetering on the edge. The film’s ambitious narrative structure and visually arresting sequences call for more in-depth recognition of the movie. The engaging storyline, dynamic characters, and cinematic beauty combine to make this film an experience not to be missed.

1 Primer (2004)

A scene from Primer (2004)
IFC Films

Primer is the greatest time travel film you’ve never seen. It’s an indie film because of its production value and shoestring budget, but it’s infinitely better than others in its subgenre. Regardless, it’s a cool movie with a dark tone that we would never associate with sci-fi because of its uncommon realism. To call it a mental mindf**k is an understatement.