Here's a few adventure hooks--or curveballs, rather--that you can throw into your games for those times player character complacency and carelessness crests and the GM seizes the moment.
1. A found device, weapon, or spaceship awakens to send a signal to mated piece with which it intends to combine. If successful, this process will dramatically alter the object's properties/abilities. Examples include: a spaceship that combines with other technology and takes on new functions; a ring that combines with its twin to give the wearer new-found superpowers--or terrible curse; or your last trip to the starship repair shop included a few "upgrades" only your mechanic knew about, like your ship is actually part of a giant super robot. Or, ya know, it could just be your everyday alien cube seeking its long lost key to unlock a dimensional gate to who-knows where/when in the spacetime pony show.
2. Speaking of inter-dimensional superdickery, the heroes begin inexplicably popping back and forth between locations (local, intergalactic, or otherwise) at inopportune moments by a dimensional portal, disguised as an everyday object. Involuntary teleportation runs unchecked until they figure out what the item is and how to deactivate it. Or worse, how to appease it--as it's actually a sentient lifeform and it's not happy!).
3. Speaking of self-aware, seemingly innocuous space objects--take a natural object in space and bring it to life! An asteroid that's perturbed by an infection of parasitic Earthmen trying to colonize it's backside; a tennis ball-sized, loudmouth of blackhole with an insatiable appetite for densely-packed matter and bad puns; a well-meaning quasar just dying to reveal the secrets of the universe to anyone who will listen, but unintentionally annihilates anything (Chris-Farley-style) in it's output path (Augh! So sorry! Did I blast you just then? I'm such an IDIOT!); or maybe it's fickle photon particles that guide heroes when they need light down a darkened tunnel or concentrate into a laser when they're too close to discovering the ancient crystal that powers them.
4. Mushrooms! Worked in D&D--they're the ultimate psychedelic/weird plot device. Why not make an entire planet of fungus that hates people? Make them glow in the dark and really smelly, per standard cliches. But perhaps space spores piloted by small blue aliens are invading all civilized planets and planting giant mushrooms that churn out billowing toxins to de-terraform your homeworld into something more habitable for themselves.
5. Check your looks in a mirror universe. The heroes find themselves in a world where an enormous, gentle Cthuloid overlord is caretaker to his fanatical human "children" who want to kill everybody who doesn't "love him" (that'd be you and your buddies). Perhaps Emperor Palpatine's efforts to establish the first Galactic Republic are in desperate need of your assistance when a band of imperialist Jedi swine make for a coup d'etat. Or the Atlanteans rise to share their enormous kelp crop only to find to surface dwellers are launching an invasion force and start by drilling into the seabed (don't scoff, it could happen!).
6. And then there's the everyday, ho-hum, conventional weirdness: the frog plague is really raining hypnotoads; the latest mutagenic radiation/biologic agent is spread by computer virus or hilarious viral YouTube video (don't ask me how that works--it's sci-fi!); or the fabric of Vulcan society breaks down and they launch a massive, psychic, holy war on all inhabited worlds with greater efficiency and devastation than the Borg. Oh, and Yoda is their president. And when 900 years old Vulcans turn--they all look exactly like him. (Seriously, it makes a lot of sense doesn't it?).
There's some ideas. Now go and be fruitful and multiply your rolls by a factor of 4. I'm exhausted and going to bed!