When Stewie and Brian go to the Disney universe and some other universes they are affected by the universe changes. But when they go to others, including the dog universe, the Japanese universe, and the two head universe they weren't affected.
Whenever Brian and Stewie went to another Universe there was always two versions of them, but when they went to the Disney universe, there was only one version of themselves.
Stewie's prediction about Brian's reaction to seeing Lois in the first alternate universe is changed in the Adult Swim version. On Fox Stewie's line is "put your penis in a wheelchair", on Adult Swim it was altered to "Your penis would shoot right off"
In the fire hydrant universe, Brian's dog tag briefly disappears.
In the Two-Headed Universe, while most characters' happy head was on the right and the sad head was on the left, Stewie's heads were the other way around.
The Sistine Chapel should not exist in a universe without religion.
Here are the universes Brian and Stewie visit:
* A futuristic universe where Christianity never existed and the Earth became more advanced.
* A universe based on The Flintstones.
* A universe where the USA never dropped the Atomic Bomb on Hiroshima, Japan meaning that the Japanese never surrendered.
* A universe where everyone has two heads: a happy head and a sad head.
* A universe that is mostly ice.
* A universe where everyone has to take a poop just now.
* A universe where everything is drawn by Disney.
* A universe based on Robot Chicken.
* A universe where Frank Sinatra wasn't born to influence John F. Kennedy's election, Richard M. Nixon won the election and botched up the Cuban Missile Crisis plunging the Earth into World War III, and Mayor McCheese was assassinated by Lee Harvey Oswald.
* A universe where everything is blocky and crudely-drawn.
* A universe that is mostly fire hydrants.
* A universe that consists of homosexuals.
* A universe that is live-action (Brian is depicted as a Labrador Retriever).
* A universe where everything is animated like a Washington Post political cartoon.
* A universe where it's only inhabitant is a far away guy that yells compliments.
* A universe of misleading portraitures.
* A universe where humans and dogs have switched roles.
When Stewie and Brian go to the universe where everyone has two heads you can see a portrait of Chris with just one head.
(While in the Disney universe)
Stewie: Brain we could spend the rest of our lives here. It's perfect.
Brian: Sounds good to me. Doesn't seem to be a thing wrong with this place.
Mort: Hello everybody.
Everyone: JEW!!! (They grab Mort and beat him up offscreen)
Stewie: Oh yeah I forgot, we're in a Disney universe.
Lyrics to "It's a wounderful day for pie."
Peter: It's a wounderful day for pie. You can ask all the birds in the sky. And they'll answer real sweet. With a musical tweet.
Quagmire the bird: It's wounderful day for pie.
Chris and Meg: For pie.
Quagmire the bird: For pie.
Lois: For pie.
Joe the kettle: For pie.
Stewie: This wounderful Brian. Let's live in this universe.
Brian: Gosh, it's pretty intoxicating isn't it?
Stewie: I want to hear more music about pie.
Peter: It's a wounderful day for pie.
Cleveland the skunk: Cause a lot better than I.
Adam West Mouse: Everyone in the house.
Peter: And this Adma West Mouse.
Bees: The bees making honey.
Tom Tucker Bunny: This Tom Tucker Bunny.
Everyone: We all sing with glee. Cause we all agree, it's a wounderful, wouderful day for pie.
Herbert the witch: You want a nice shiny red apple to put in that pie.
Everyone: No! (They all pelt him wiht pies)
(in the Robot Chicken universe)
Stewie: (to Chris) How does it feel to be on a major network for 30 seconds?
Chris: F**k you!
Brian: Okay, I'm a new neighbor, and you're my pet human, Hotchkis, got it?
Stewie: (stammers) I'm not so crazy about "Hotchkis" anymore.
Brian: What do you mean? You came up with Hotchkis.
Stewie: Eh, I know, but how about Axel or Maximillian or Dex? You know, it's gotta have an "x" in it 'cause that means I have cool parents who take me on expensive ski trips on spring break and I get to drink wine with dinner even though I'm only 14 and--
(Brian rings the doorbell)
Dog Peter: (scampering to the door) Omigod-i-know-that-sound-it-means-theres-a-potential-intruder-at-the-front-door-or-one-of-my-pals-either-way-im-excited-and-ready-for-anything!! (opens the door) Hello!
Brian: Hello, my name is Blake Carrington.
Brian: And this is my human, Gabe.
Stewie: Aw no, what?!
(Brian and Stewie appear in an alternate universe filled with red fire hydrants.)
Brian: Love it!
Stewie: Hate it.
(They transport to another universe, filled with a bunch of a strong, nearly naked guys.)
Stewie: Love it!
Brian: Hate it!
(Brian on seeing a hotter version of Meg)
Brian: My God! Is that Meg?
Stewie: 36D Brian. And you know what's amazing? In this universe, she is still one of the ugly ones. If you saw Lois, you would have to put your penis in a wheelchair.
Carnival Barker: Step right up, step right up! You won't believe your eyes. Step right up and see the amazing half man, half clam.
Peter: (coming out of the tent) What a ripoff, it's just Kim Cattrall sitting Indian style.
Quagmire: (leaving a woman's house) Thanks honey, say hi to your husband. (device on his belt beeps) Oh, I've got AIDS again, better take my NyQuil Cold, Flu and AIDS. (takes pill) All gone!
When Stewie was explaining the "Multiverse Theory" to Brian, he used the phrase "The theory states that there are an infinite amount of universes coexisting with ours on parallel dimensional planes.".
This was very close to how Captain Kirk described the mirror universe in the "Star Trek" episode "Mirror, Mirror" when he, Uhura, Scotty and McCoy were transported into the parallel universe in that episode.
Snow White and the Seven Dwarfs:
Lois and Herbert are dressed like Snow White and the Evil Queen as a Harmless Peddler Woman respectively, as they appeared in Walt Disney's 1937 animated movie.
The Little Mermaid
Meg Griffin, in the Disney Universe, is reminiscent of Ursula the sea witch from Disney's The Little Mermaid.
Brian and Stewie travel through parallel dimensions using a remote-control like device, similar to this 1990s science fiction show.
Stewie: Gosh Brian, I sure hope this next leap will be the leap home.
A parody of a famous line from the Television series Quantum Leap.
Planet of the Apes
Stewie: Take your stinkin' paws off me you damn dirty dog.
This is a parody of a line that Charlton Heston's character says in the film Planet of the Apes.
Stewie tells Brian that the Sistine Chapel ceiling was painted by John Hinckley instead of Michelangelo. Looking up, it's a collage of photos of Jodie Foster. Hinckley, who was obsessed with Foster, attempted to assassinate president Ronald Reagan to win her affection.
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