The game's story begins when during the Springfield's Elementary School science fair, Bart wanders into a virtual reality simulator from one of his classmates. There, Bart experiences several virtual levels he must complete to escape the machine:
- Dino Bart: Bart is a dinosaur in a primeval Springfield, he must fight for survival against other dinosaurs and primitive versions of other Springfield citizens.
- Baby Bart: Bart re-lives his days as a baby, where he escapes his crib and swings over all the neighborhood.
- Class Picture: Bart becomes determined to ruin the class picture by throwing tomatoes and eggs at his classmates from a hiding place.
- Mt. Splashmore: Bart rides the water slide and must find the exit amidst all the twists and turns.
- Doomsday Bart: The Springfield's Nuclear Power Plant has suffered a meltdown and Springfield has become an apocalyptic wasteland, Bart must race home in his bike avoiding dangers.
- Pig Bart: Bart is a pig who must escape from Krusty's Pork Factory.
Virtual Bart provides examples of:
- All There in the Manual: The game's manual states that the virtual reality system was created by Bart's classmate Martin, and was intended to be harmless educational fun, until Bart tampered with it. None of this information is provided in the game itself which even contradicts the manual by implying that Bart was tricked into entering the simulation.
- Amusement Park of Doom: The water slide featured is excessively long and deadly. Ways you can die include falling out into a canyon or head first into a wall.
- Animorphism: Bart turns into both a pig and a dinosaur.
- Anti-Frustration Features: The Bonus Space at the top of the wheel rotates between an extra life and loss of a life, but will always be an extra life if Bart has none left.
- The Apunkalypse: One of the simulations takes place in a Mad Max-esque dystopia following an explosion at the nuclear power plant where Bart and the bullies are seen in punk style clothes.
- Baby Morph Episode: One of the games involves Bart searching for an ice cream van after turning into a baby.
- Ball-Balancing Seal: The third section of the Baby Bart level takes place outside a circus tent. Behind a fence are a colony of performing seals that pop and down, balancing balls on their noses. Bart must hop across the balls when they pop up without falling onto the ground below so he can make his way into the circus tent, which forms the fourth and final section of the level.
- Ballistic Bone: In the Dino Bart level, the prehistoric versions of Marge and Maggie toss bones at Bart.
- Balloonacy: Near the end of the first section of the Baby Bart level, Baby Bart comes across a bunch of balloons, which he can use to float above the hazards of the fence.
- Bonus Space: The seventh space at the top of the roulette alternates between a corn dog and a skull and crossbones. If Bart lands on a corn dog, he will get an extra chance, and if he is on his last chance, the top space will remain at a corn dog. If he has four chances, however, the top space will remain at a skull and crossbones.
- Carry a Big Stick:
- In the Dino Bart level, the caveman versions of Homer and Krusty carry clubs.
- One clown mook type in Pig Bart wields a large mallet that both deals a lot of damage and stuns Bart.
- Corrupt Corporate Executive: The three Executives of Krusty Corp who hold the rest of the pigs captive at the end of Pig Bart.
- Dual Boss:
- Homer and Moe's boss battle at the end the of Dino Bart level.
- The three executives fought at the end of Pig Bart.
- Egging: The second half of the Class Picture level has Bart throw eggs at his classmates.
- Eternal Engine: The entirety of the Pig Bart level takes place in Krusty's Pork Factory, where Bart has to save the other pigs from being turned into ham.
- Everything Trying to Kill You: In the Baby Bart level, birds, squirrels, bouncing balls, flying freezebes, cats, and angry dogs want a piece of baby Bart.
- Expressive Health Bar: Carried over from Bart's Nightmare, Bart has a health meter which also depicts his relative status. At full health, he seems confident. As his health drains, he turns green or grey and begins to look sickly, and when he reaches critical health or dies, he becomes a skeleton.
- Gameplay Roulette: A literal example; the stages are randomly selected by virtue of Bart being strapped to a wheel.
- Goomba Stomp: Dino Bart and Pig Bart can do this to enemies, in the latter it's the only way to eliminate them.
- Hailfire Peaks:
- Dino Bart has a section inside a volcano and a frozen river as the last one.
- Pig Bart, similarly has a section inside a freezer and another inside a furnace.
- Baby Bart has tree swinging all over the neighborhood, then a baby carrier cart section, and finally a circus.
- Help, I'm Stuck!: If you go down the wrong paths of the Mt. Splashmore level the first two times, you'll come across a stuck Homer. This prevents Bart from losing a life or having to start the level from the beginning. The third time, Bart is on his own.
- Here We Go Again!: In the good ending, Bart exits the machine and leaves the place, but next in line is Homer, who is then strapped into it.
- Human Cannonball: The Baby Bart level ends with Baby Bart landing in a cannon at the circus, which fires him into the ice cream truck he has been pursuing.
- Human Popsicle: In the ending of Dino Bart, it shows caveman Homer encased on a block of ice and on display in a museum.
- Improvised Parachute: In the Baby Bart level, Baby Bart can use his diaper as a parachute to slowly descend.
- Inside a Computer System: The premise is that Bart is trapped inside a virtual simulation where he needs to complete all its levels to leave.
- It's a Wonderful Failure: Failing any of the VR scenarios (with the exception of Baby Bart) shows a cutscene of the consequences:
- Using up all of Bart's ammo in Class Picture results in him wearing his Sunday suit in the picture and looking unhappy.
- Alternatively, if you hit any school faculty (except Skinner if he's bending over in the S-NES version), Bart will look extremely nervous as his teacher and principal give him some very nasty scowls in the picture.
- In Dino Bart, it shows a paleontologist finding Bart's fossilized remains.
- Mt. Splashmore can end with Bart plunging into a gorge, or slamming into (or through) a brick wall with Krusty's face on it. Bart can also get eaten by a lion, but it will belch him back out into the slide, effectively giving him another chance.
- Pig Bart shows Homer eating a box of corndogs, one which has Bart's face, Homer looks at it for a moment then shrugs and eats it anyway.
- In Doomsday Bart, Bart has his arms stretched by Jimbo's gang.
- Running out of lives results in Bart being booted out of the VR machine and becoming sick as Nelson laughs. Cue Game Over.
- Using up all of Bart's ammo in Class Picture results in him wearing his Sunday suit in the picture and looking unhappy.
- Kill It with Ice:
- A clown mook type carrying a liquid nitrogen tank will attempt to freeze Bart in the freezer section of Pig Bart.
- Dino Bart defeats Homer and Moe by knocking them down into a frozen river.
- Lead the Target: In the Class Picture scenario, the player must calculate the distance for the throw and account for the movement of Bart's classmates. In the second stage the characters now move diagonally which adds difficulty.
- Mighty Roar: Dino Bart can roar and eliminate all enemies on screen.
- Monster Clown: Clowns act as enemies in the Pig Bart scenario.
- Multiple Endings: The Class Picture level has different pictures depending on how many students you hit, or if you hit an adult. On the SNES version, if you manage to hit all the students and Skinner while he's crouching, Bart moons the camera.
- Mythology Gag:
- The Baby Bart level is based on the flashback scenes in "Lisa's First Word". The ice cream truck that Baby Bart pursues and lands in at the end of the level is "Native American Ice Cream (Formerly Big Chief Crazy Cone)" from "Itchy and Scratchy: The Movie".
- The Class Picture level is based on a gag in "Duffless" where Bart tosses Lisa's giant tomato at Principal Skinner as he crouches down to tie his shoe, Skinner even makes the same pose during the level. While you must avoid hitting the adults, hitting Skinner while in this pose rewards the player with additional ammo.
- The Mt. Splashmore level is based on "Brush With Greatness", taking place in the H2Whoa! water slide and having Homer get stuck in the wrong paths the first two times. The bad endings (see It's a Wonderful Failure) are also a reference from "Bart the Daredevil".
- Doomsday Bart is similar to the Treehouse of Horror VIII segment "The Homega Man", which aired three years after this game's release.
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Nintendo Hard: The leap to 16-bit and being a sequel/followup to Nightmare didn't end the tradition of extremely tough Bart based Simpsons games. While the different game play styles for each level are unique, they are selected at random, there are no saves or passwords and you can lose a life by complete random chance when Bart is spinning on the wheel. The levels are pretty long as well and require lots of trial and error. The controls are generally average to bad (especially the Picture Day level) and it's hard to get them down unless you use practice mode, which is a nice feature...but having to play the game in one go, it can be hard to master all six control schemes at once. - Our Founder: In the Pig Bart level, just before the battle with the executives guarding the captive pigs, a framed picture of Krusty's head with the words, "OUR FOUNDER" on the plaque of the frame can be seen, as well as busts of Krusty's head.
- Picture Day: One of the simulations takes place during picture day for Bart's class, and the goal is to hit everyone with tomatoes and eggs, so that the class picture will be ruined for everyone except Bart.
- Platform Hell: The circus section in Baby Bart has a lot of jumps including timed jumps on the trapezes, mis-time one jump and Bart will plummet to its doom.
- Power-Up Food: Corn dogs restore lost health.
- Prehistoria: Dino Bart of course. In which Bart is a dinosaur and has to face other dinosaurs and caveman versions of his family, as well as Moe, Barney, Krusty, Smithers and Mr. Burns.
- Produce Pelting: The first half of the Class Picture level has Bart throw tomatoes at his classmates.
- Racing Minigame:
- Doomsday Bart, in which Bart must race home in his motorcycle, avoiding many dangers.
- Baby Bart has a racing section with baby strollers.
- School Setting Simulation: The Vandal level takes place outside Springfield Elementary School during recess. In this level, Bart hides in the bushes and tosses tomatoes and later eggs at his classmates so that he will look good in the school photo by comparison. The level ends if Bart hits all of his classmates, runs out of tomatoes or eggs, runs out of time, or hits one of the adults (though he can hit Principal Skinner while he is crouching).
- Screw This, I'm Outta Here: If you hit an adult in Class Picture (except Skinner if he's crouching in the S-NES version), Bart says, "Oh no! I'm outta here!" and the mini-game ends early.
- Skewed Priorities: In Doomsday Bart, the reason Bart is racing home is to catch Krusty's show on TV.Bart: Just in time!Krusty on TV: Hey surviving kids! Hehehaha!
- Slide Level: In the Mount Splashmore level, Bart must choose the correct paths of the H2Whoa! water slide (indicated by the stripes on Groundskeeper Willie's bathing suit) while dodging the other patrons. The first two times Bart goes down the wrong path, he is saved by Homer, who is stuck. If Bart goes down the wrong path a third time, he is either sent back to the beginning of the level or to a path that costs him a life. The level also has a time limit, but Bart can add more time to it if he collects clock power-ups.
- Squashed Flat: This can happen to Bart in the Doomsday Bart level if Otto runs over him with his bus.
- Stripped to the Bone: At the end of Doomsday Bart, Bart arrives home and joins the skeletal remains of his family on the TV couch.
- Tail Slap: Dino Bart can attack with this.
- Temper-Ceratops: Triceratops are among the enemies in the Dino Bart level.
- Timed Mission: Each level has a time limit, but in the Mt. Splashmore level, Bart can find clock power-ups to add extra time, and in the Doomsday Bart level, passing checkpoints adds extra time.
- Whammy: The top space on the roulette alternates between a corn dog and a skull and crossbones. If Bart lands on a skull and crossbones, he loses a chance, and if he is on his last chance, the top space will remain at a corn dog. If Bart has four chances, the top space will remain at a skull and crossbones.
