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When returning to the Sector 5 Church, two different images of Aeris may be seen. One appears for a split second in the center of screen before disappearing, while in the other Aeris is seen tending the flowers before Cloud moves closer. It has been speculated this is meant to be her "ghost".
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During the cutscene Spoiler:in which he kills Aeris, Sephiroth's hands are bare as he descends from the ceiling. However, during the rest of the scene, he has black gloves on.
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Aeris, after being brought back via a cheat device, has dialogue in discs 2 and 3. This seems to imply that either Spoiler:she was not meant to die at the end of disc 1 or that Spoiler:she was intended to be revived later in the game.
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Attachment After you find Cloud in the hospital after he falls in the Lifestream, he will mumble incoherent things when you speak to him. One of the things he mumbles is "zeno... gias..." This is a translation error and a reference to the game Xenogears. In the PC port of Final Fantasy VII, the spelling is corrected to "Xeno... gears".

Cloud also says "A billion mirror fragments.... small.... light..." which is a reference to the vocal song of Xenogears, Small Two of Pieces. One of the lines to the song is "Broken mirror, a million shades of light".
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While at the Honeybee Inn, if you look into one of the occupied rooms through a key-hole, you can see a mini Cait Sith inside a bath tub jumping around.
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Cloud's hair was originally supposed to be black and slicked back to contrast with Sephiroth's long white hair. The developers also thought it would be a good way to render less polygons on screen. The idea was eventually ditched for his iconic spiky hair. The idea was later used for Angeal, the original wielder of the Buster Sword and Sephiroph's close friend in Crisis Core.
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Attachment Many people still don't know how Cloud's legendary "Buster Sword" sticks to his back, but if you look at his initial design, it shows there is a magnet held by his pant straps that keeps his sword in place.
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During development, series creator Hironobu Sakaguchi's mother passed away. At the time, Sakaguchi wanted to craft a story that would show just because somebody has passed on, it doesn't mean that they are forever lost. He also wanted to present a realistic death, rather than a Hollywood sacrificial end. These two desires resulted in the concept of the Lifestream and Aeris' iconic death. The characters continuing to go on, attempting to save the world, after Aeris' death is a reflection of his own feelings coping with his mother's tragic death.
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Attachment During the scene where Sister Ray is about to fire the Diamond Weapon, there is a voice that comes through the intercom. The voice actor is not credited in the credits, and the person who spoke through it is unknown.

Although a voice was heard, and ultimately makes Final Fantasy VII the first Final Fantasy game with a voice actor.
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The original idea for the game had it set in modern New York City in the year 1999, and was intended to have a "detective story" theme, with a character called "Hot Blooded Detective Joe". The early script had him chasing the main characters, who would then blow up the city of Midgar.
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Attachment In the Japanese version, the test battle in the debug room features a proper background and models for the enemies included (borrowed from other enemies), whereas the international version simply pits the party against yellow pyramids in a black void.

Additionally, the very first Japanese release contains an unfinished eleventh section of the debug room, left over from an earlier build of the game. Because the game's code changed significantly since that build, much of the eleventh section is broken: Cloud's model does not show up (though he is still able to move around and interact with the NPCs there), text is corrupted, and the background music is a heavily distorted version of Aeris' theme.
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A hidden programmer message is hidden in the files of Disk 3, stating:

"great special thanx to you, ARIKO...from your husband, HIDEJI".
subdirectory_arrow_right Final Fantasy VII Rebirth (Game)
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Attachment In the very first Japanese release of the original game, at the bottom of the well in Corel Prison, a rare debug enemy known as "Test 0" that was accidentally left in the game on its initial release can be randomly encountered. This encounter does not require cheats or hacks to occur, although GameShark codes can be used to access every other debug enemy battle in the game. This battle was removed from all future releases of the game. "The Completely Unauthorized Final Fantasy VII Ultimate Guide" by Versus Books, released in 1997, features an entry on this enemy (note that the HP listing in the guide scan is incorrect; Test 0 has 30000 HP).

Final Fantasy VII Rebirth nods back to this oversight by making Test 0 a legitimate optional encounter in the Beast Battleground. The nature of its presence in the original game is referenced in the enemy's bestiary entry, which describes it as "A test subject that managed to escape Shinra's R&D Division due to a developer's oversight."
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YouTube video showing the Test 0 battle in the original release:
https://www.youtube.com/watch?v=bxYBDikspc4

[Below sources and additional info provided by VinchVolt.]

TheGamer article about the Test 0 battle's inclusion in Final Fantasy VII Rebirth:
https://www.thegamer.com/final-fantasy-7-rebirth-references-the-original-test-0-glitched-boss-easter-egg-jp-release-ps1/

Twitter post featuring a screenshot of Test 0's bestiary entry in Final Fantasy VII Rebirth:
https://x.com/TheStrifeisRife/status/1767725768279265660
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According to the game's art director Yƫsuke Naora, he liked how his design of the city of Midgar turned out, having envisioned the city in his head as a pizza while he was designing it.

After the first AVALANCHE mission at the start of the game, Barret will reference this inspiration when talking to Cloud about the upper plate of Midgar:

Barrett: "The upper world...a city on a plate...It's cuz of that &^#$# 'pizza', that people underneath are sufferin'!"

Additionally, the name of the song "Underneath the Rotting Pizza", which prominently plays in many of the slum areas in Midgar, is a reference to its design.
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According to character designer Tetsuya Nomura, Aerith's dress was specifically designed so that it used a low number of polygons. Cloud was originally designed with slicked-back hair for the same reason.
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Attachment There is a hidden "Red Man" in the Corel Prison. The model is hidden from view in normal gameplay. There are no other models like this in the game, and it is thought to be a signature from one of the designers.
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The number 7 is very prevalent in the game.

• AVALANCHE resides in Sector 7 of Midgar.
• Tifa's bar is called 7th Heaven.
• At the start of the game, seven people are either living or staying at the 7th Heaven -- Cloud, Barret, Tifa, Marlene, Biggs, Wedge, and Jessie.
• The books in the Shinra Mansion library shelves form the letters "VII".
• The red plane in Costa Del Sol harbor has "VII" painted on the side.
• The Gold Saucer has seven areas of attractions.
• The Ancient Forest has seven treasures.
• The Turtle's Paradise awards seven items for completing the flyer-hunt sidequest.
• Aeris and Ifalna were held captive by Hojo for seven years.
• It's been seven years since Cloud left Nibelheim to join SOLDIER.
• Tifa spends seven days unconscious before waking up after the Weapons awake.
• Red XIII tells the party that Meteor will reach the Planet in seven days.
• Cloud levels up to level 7 in the first battle.
• If a unit's HP hits 7,777 during battle they enter All Lucky 7s status.
• The "lucky" handicap reel on the Battle Square is called Lucky 7.
• Most characters have seven different Limit Breaks. The exceptions are Cait Sith, who has two but with various different outcomes, and Vincent, who has four, but each form has two special attacks. This makes for seven characters who have seven Limit Breaks.
• There are nine main playable characters, but only seven are mandatory.
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Attachment One of the early art directions of the game was going to use 2D pixel-based graphics. There was one concept image early in the development featuring an isometric view in this style using Final Fantasy VI character designs, including Locke.
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Red XIII had a subplot that was cut from the game as the plot developed in a different direction. Originally there were to be two Red XIII clones created by Hojo called Cobalt XIV and Indigo XV. The player would have to fight all three of the "Red XIIIs" and figure out which was the real one, with the three swapping places periodically. Defeating the real Red XIII by accident meant the player had to fight the following boss battle with Hojo with only two party members. Cobalt and Indigo would return in the final dungeon of the game, turned into cyborgs and determined to prove they were superior to the real Red XIII.
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According to the Final Fantasy VII Ultimania Omega, earlier drafts of the game's scenario involved three characters known as the '3 Saints'. Not much is known about their original role in the story, other than they were kidnapped by Sephiroth, and that Red XIII knew more about them than the rest of your party. The only Saint mentioned by name was called Gandalf, who was captured by Hojo and "practically crippled" in a Shinra laboratory.
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