The story picks up where the first game ended. After Zak and the Cyberia weapon crash land back on Earth following the destruction of Devlin's orbital headquarters, they are intercepted by an FWA team led by a Dr. Corbin. Corbin, under orders from his FWA employers, places Zak in cryo-storage and uses the remains of the Cyberia weapon to create a deadly virus called nano-toxin. Though the FWA seeks to quell a growing rebel movement with the nano-toxin, the maniacal Corbin intends to use it to kill millions and "reshape the world as we know it."
After three years in cryo-storage, Zak is thawed out by a renegade FWA major, and together the two of them set out to find Corbin and stop his plans.
This Video Game contains examples of:
- Big Bad: Dr. Corbin. One has to wonder what he did to Zak as he is featured rather prominently and in an exaggerated fashion within Zak's dream sequences.
- Bus Crash: You learn at the beginning of the game that the Cyberion was removed from Zak and chopped up by Dr. Corbin to create his nano-toxin, making the first game something of a Shoot the Shaggy Dog story.
- Dream Sequence: There are a couple, of rail-shooter variety; you still have to pass them to advance the story.
- Everything Trying to Kill You: The good news is that there are arguably fewer ways of getting you killed compared to the predecessor; the bad news is that for the methods that still can get you killed, they tend to happen more easily.
- Evil Laugh: Dr. Corbin again. And he isn't shy to demonstrate it at all.
- Guide Dang It!: Accessing data terminals during the on-foot portions of the game can involve some very frustrating puzzles; and while the goal is usually to look for specific information, instructions tend to be vague enough that players often resort to browsing every entry within and hoping they get lucky.
- Hollywood Hacking: Graham, your Mission Control guy, can proceed to extract the security codes of an installation's perimeter defenses right as you watch its demonstration video.
- Human Popsicle: Zak was put into this position, but he was brought out of it three years later.
- Hypocrite: Zak seemed surprised when Major kills a FWA guard to cover his escape five minutes into the game. Players who have played the first game might have better memories of the body count he'd left in his own wake prior to getting stuffed into cold storage. Or what he is about to do after getting thawed, for that matter, since this is Cyberia after all.
- Imperial Stormtrooper Marksmanship Academy: Averted in rail-shooter and on-foot segments, since you aren't even given the option of taking cover this time around.
- Mad Scientist: Dr. Corbin is so obsessed with creating and perfecting nano-toxin that it's all he cares about. He'd be easily furious over any problem with shipments of materials he needs to that end but has shown no apparent concern toward the rest of his own fortress (also one of FWA's most important weapons development sites) falling apart.
- Time Skip: This game takes place three years after the events of the first game.
- Violation of Common Sense: Mostly downplayed when compared with the first game, although it can still crop up at times. One example is during the last 'buggy' scenario, where you are travelling down a tunnel filled with landmines while being pursued by enemy hoverbikes. Although there are many landmines, the amount of damage they inflict individually is low when compared to the enemy turrets, hoverbikes and attack buggies in your way, not to mention that your buggy is able to steer clear of many landmines that aren't directly in front of you, as Zak lampshades during the beginning of the scenario.