It is never explained why there is a painting of Ib's parents in the fabricated world.
That might have been a hallucination on Ib's part. When she mentions it, Garry seems surprised and asks Ib if the painting really depicts her parents. After a moment of silence, he agrees with her, but worriedly notes that the gallery is affecting even a strong girl like her to such an extent.
It is also never explained who could have written the creepy writing in the room with the "Separation" painting.
Due to how flammable art can be — particularly oil paintings — and the way you end up defeating her, it is very likely that Mary wrote all over the room.
That, and did you notice the red footprints lead out of the room with "Separation" and towards the hall with Mary?
If you examine the mirror after that scene, there's a chance that you'll see "NO FIRE" written everywhere.
A weird bit of Gameplay and Story Segregation. Soon after Mary joins, your party gets split up and Mary and Ib go one way while Garry goes another. Ib and Mary end up on the floor right above where Garry is, and solving the puzzles leads to them unknowingly helping each other. It gets weird when there's a picture of a painting that Ib and Mary have to enter the title of. The actual painting is on Garry's floor, but he has no way of telling them about it or even knowing that they need that information to begin with. It goes the other way too; Garry has to say when a certain painting was made. This information is found in a book that Ib and Mary read. Again though, they're split up and they have no idea Garry's right under their feet, much less that he needs to know about the age of that juggler painting they just read about.
Garry, Ib, and Mary have the primary colors of paint as their rose colors in an art-themed game.
While red, blue, and yellow are famously known to be the primary colours of pigment, the primary colours of light are red, blue, and green which are reflected by either the stems of the roses or the way Mary's dress is green. Though Mary's yellow rose is the odd one out, she is still trying to appear like she belongs.
If you try to look into a mirror with Mary in your party (which you probably won't, since it involves otherwise pointless backtracking), the mirror shatters.
When Ib is with Mary, she almost never runs into enemies. It's because Mary's also a painting, and wants to escape with Ib. Also, the other artworks are like family to Mary.
The painting that uses unnatural vines to separate Garry from Mary and Ib is the Flowers of Jealousy. Mary also uses vines to protect her things and her yellow rose can mean envy or jealousy as well as friendship.
It's also shown in "A Painting's Demise" that the other paintings don't approve of Mary leaving (writing on the wall calls her a bad girl). The Flowers of Jealousy are jealous that Mary is going to leave.
The painting of a figure in brown was not killed for helping Ib, but for telling the truth, of all things, in the Liar's Room.
The Ladies follow you around almost hungrily in the gallery because Guertena based them on Gold Diggers he met in his life, and as a result they are greedy just by their nature.
If you head for the Bonus Dungeon while Garry is with you, Garry comments that he feels like he's been by those stairs before. This sounds odd, as Ib's never seen those particular stairs in her life, but then you realize those stairs lead you to an alternate version of the Lady in Blue's hallway.
Some of the dialogue you might get when talking to Garry after returning his coat also has him mention having difficulty remembering how exactly he got to the alternate gallery, but mentions that he saw some stairs where there had been a wall before.
If you're on the path for "A Painting's Demise", you briefly get to play as Mary. There is no rose in the upper left-hand corner. Because she doesn't need one; her Soul Jar is her painting.
Ib sometimes sees rabbits instead of dolls. If you fall asleep on "Final Stage", you see some of Ib's memories, and learn that her bedroom is full of stuffed rabbits and she's very fond of them. So that's why she keeps seeing rabbits!
You'd think Mary would be angrier at you for winning the doll room than failing, since failing is in her interest as it causes Garry to forget her secret, while winning it leads to Garry stopping Mary from attacking Ib. But failing is the highest weighted action that adds to the counter that decides whether Mary's angry enough to kill Garry at the end. If you succeed, then when Garry stops Mary, she's still having a breakdown, so she's too upset to be angry, whereas if you fail, Mary either didn't have a breakdown at all or has had time to calm down. She's less scattered, so she can be properly angry. About Ib bringing Garry to his senses. And Garry handling Mary's rose. And Garry knocking Mary out. And Garry going and remembering Mary's secret anyway.
The new endings provide another reason why Mary wants to make friends with Ib so quickly and can only leave with her. In "A Painting's Demise" Mary refers to "The Lady In Red" as her big sister. Since Ib and her mother look a lot like "The Lady In Red" Ib reminds Mary of her "big sis" and in "Together, Forever" Ib ends up being Mary's big sister in the real world as well.
Garry's rose has 10 petals on it. Since it's an even number, the last one would always be "loves me not", except then Mary counts the stem to get "he loves me".
During her mental breakdown Mary has a chance of mentioning a special trick to always get "loves me"; count the stem if you end on "loves me not".
You don't see anything through the peephole in that one door in the purple area. The statue peering back doesn't have a head.
There are a couple of things about Ib, Mary, and Garry that hint at the nature of the endings: You can only save one or the other, not both, no matter what you do; many things connect them in pairs, but few, if any, that connect all three.
The roses. Mary and Garry's are both "unreal". Mary's rose is from her painting and no more real than she is, but blue roses don't exist in nature. Ib's is real, and can pair with either "real" rose, or is the one left out if both are taken as unreal.
Their names. Mary and Garry rhyme; Ib (pronounced "eeb" and identical in Japanese to "Eve") and Mary share a Biblical origin; Ib and Garry are alternate spellings.
Their depictions in and connections to artwork. Garry and Ib are both depicted in paintings (if depicted at all) as being dead; Mary and Ib are both depicted with roses (the same rose, in fact, in the A Painting's Demise ending), Garry and Mary are both emotionally connected to a specific work (Mary has her own painting; Garry is drawn to the Hanged Man from the very start of the game), plus both have the ability to move the headless statues.
In the bunny room, you can read a book that talks about how a person spiritually suffering will hallucinate and be destroyed, all while not being conscious of it. Not only it references how Ib sees the creepy dolls as cute bunnies, along other things, but it foreshadows what happens if you sleep too much on the Final Stage, in the hidden gallery: you dream of an happy life to escape the reality of the gallery, then you don't wake up.
People whose roses are injured in the painting world are wounded. But when Ib finds Garry after Mary finishes plucking his rose, she comments that he looks like he's just sleeping. Ib is known to hallucinate. Wanna bet she subconsciously censored what actually happened to Garry?
The endings "Ib All Alone": Depending on how you've completed the game, you discovered the portrait that leads back to the real world with Garry. Even though you decide to jump into the painting, Ib's mother arrives and scolds her for running off with strangers. You can choose to either go with Ib's mother or head back to the real world with Garry. If you choose to stay, Ib will follow her mother, only for a static Scare Chord and a split-second screen black-out to reveal that Ib is following nothing, all while Garry is calling to her from within the portal. Let this sink in for a moment; you've done everything in your power to save this girl, and now she's trapped in the painting world forever, trailing an illusion she believes is her mother. Dear God...
The second version is much crueler, as Ib heads back to the portal alone, since Garry dies from exchanging his rose with Mary, who plucks the petal off of it, in order to retrieve Ib's from her. Just as you choose to go back to the real world, Garry appears and convinces Ib that the exit to go back was somewhere else. The choice to follow Garry simply ends with Ib following him off-screen, and that's it.And you don't even know what happens afterwards, or where the Fake Garry is taking Ib.
Mary has to switch places with a real human to escape the painting world, which she plans to accomplish by killing Garry. Additionally, in the endings where Garry dies, he replaces a portrait in the gallery, and a clone of him will try to lead Ib away from the exit. But what if it isn't a fake? Does being killed by a painting monster turn you into one of them?
Apparently, it is possible to lose your memory and not regain it after you leave the art world. Also, people outside the world can have their memories changed like Ib's parents in Together Forever. Guertana seemingly didn't base most of his paintings on real people, but in the Forgotten Portrait ending, Garry takes the place of the Hanged Man painting. What if some of his paintings actually ARE real people who died in the art world and no one remembers that they were real? What if this whole cycle repeats itself endlessly, with nobody on the outside world noticing that people go missing? What if the monsters that tried to kill Ib and Garry were only doing so because they desperately wanted to escape?
The painting you piece back together in the Bonus Dungeon is a man (whose face is out of frame) holding a paintbrush titled "Guertana". Garry even points out the man never did a self-portrait. Oh boy.
In one of the books, you can read about a little girl that got lost in the gallery and later died, which seemed to be based on Ib as a worst case scenario. If the above theories are true, then that girl was probably Mary, and the fact that she was Guertana's last work can create interestingimplications.
Alternatively, it's a description of what will happen to Ib in the "Ib All Alone" endings.
Or, considering the title parallels and the even closer match, the book could be referring to Mary in the "A Painting's Demise" ending.
The "Welcome to the World of Guertena" ending in 1.04. Garry goes utterly insane. Ib has a breakdown over this. Mary keeps them both trapped in her world, forever. Ib's parents and any friends or family Garry might have are never going to see either of them again. To make it even worse, in the gallery's celebration of Mary having two new friends, Ib and Garry weren't moving at all, making Mary's keeping them a possible Mummies at the Dinner Table situation to boot.
In that same ending, take note of the Lady in Blue. She is holding Garry's rose. Again.
The "A Painting's Demise" ending is full of it. Not only are any loved ones of Ib and Garry never going to see them again, but there's also the whole thing with Mary's attempt to leave. In order for Mary to be able to leave, someone has to take her place. In the ending "Together, Forever", this happens; Garry dies in the phantom gallery and Mary is able to leave with Ib. However, even though Garry and Ib both remain in the phantom gallery in the ending "A Painting's Demise", Mary's attempt to leave in that case ends up destroying her. Since neither Garry nor Ib were actually dead at the time, at least not yet, this indicates that it's not merely someone staying behind that's needed; someone has to actually die. What if Mary had managed to convince Ib to leave with her in the "A Painting's Demise" ending? Would Ib have had to see Mary die right before her eyes?
Even killing may not be enough. If the "Together, Forever" ending is any indication, it's possible that Mary also has to leave with someone from the real world to "guide" her there. Mary had the fortune of there being two people from reality in the painting world, one to kill and one to escape with... but what if she didn't and was just stuck with Garry? She would've been screwed.
If the above theory about some of the paintings being dead people from reality is true, then this means a number of paintings and past people have made their own escape attempts, all met with failure in an intentionally endless cycle. The painting world is literally being Powered by Forsaken Children!
The doll room event, the toy box, and the fact that you get bad endings by being mean to the gallery hint that the artworks have a special sort of bond with each other and are at times fiercely protective of each other, and the endings "Welcome to the World of Guertena" and "A Painting's Demise" pretty well confirm it. As well, Mary considers Guertena as a father and refers to the other artworks as siblings. This makes Mary stabbing the mannequin head during her psychotic breakdown a lot more upsetting, since she's basically hurting her own sibling. More horror kicks in when you are in the Bonus Dungeon. There are two paintings, one of them being "Mistake", who have had their faces scribbled out, and a couple of paintings are found in a completely dark room, hidden from sight. How do these artworks feel towards Guertena? Do they feel abandoned by him?
Before the 1.04 update, I had always assumed that the creepy messages that draw Ib into the gallery were left by Mary. But as we can see in A Painting's Demise, they most certainly were not. So that begs the disturbing question... who is REALLY luring innocent people into the painting world? It seems like they're doing it just for fun... Which of course means that Mary's death/escape probably isn't the end of it...
The "sinister painting" depicting Ib falling, the two potential images of hanged Ib in the Sketchbook world that only Ib can see, the fact that Ib hallucinates bunnies, which happen to be what her bedroom at home is filled with, the painting of Ib's parents, the fact that Ib dreams about memories of her birthday if she sleeps on "Final Stage"...why does the gallery tailor itself so much to Ib and seems to know things about her that it has no business knowing?
The gallery itself seems out to get Garry. The "Flower of Jealousy" painting splits Garry off from his companions. "Tattletale" and "Strained Ear" let Mary know that Garry has found out her secret. The dolls give Garry a lot of trouble and might drive him insane. And of course, Garry might die if you doomed him enough. Those can be attributed to Mary not liking him much. But then, Garry quickly gets his rose stolen and is almost killed when he steps into the "other" gallery. Obviously Mary had nothing to do with that one. If you kicked a mannequin, then you might get a "Hanged Garry" message and Garry starts feeling something around his neck. And right before the Abyssal Park section of the Bonus Dungeon, the message before it reads "Remember the artworks you hold dear".... unless you have Garry with you, in which case it says "Drown in the abyss." And it's really for certain Mary had nothing to do with that last one because by that point she's dead.
He's a guy. Almost all of the artworks are either distinctly feminine, or genderless, and the masculine ones like the Hanged Man and the Fisherman are paintings; one of them is tired to Garry himself, the other eventually ends up empty when the fisherman vacates the picture. Guertena prefers women as artistic subjects, and since the gallery is his own feeling made manifest, it may have "interpreted" Garry as a female and then reacted bitterly when it realized he wasn't.