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Being a Roguelike, The Binding of Isaac naturally requires a lot of work into making sure things interact properly without making the game screw itself up. Sometimes, though, Edmund and co really show how they thought ahead with certain things that you don't expect.

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     Original game 
  • Cain wears an eye patch. He shoots tears only from one eye, and when he acquires an item that would go over his patched eye, it's replaced with a version that's exclusive to him.
  • The Common Cold replaces your tears with poisonous mucus. If you find something that replaces your tears with something else (e.g. lasers), your attacks can still poison enemies, and most such items get an additional effect. Mom's Knife, for example, drips with green poison, and most lasers turn green.

     Rebirth, Afterbirth, and Afterbirth† 

  • The Black Candle item gives Isaac immunity to curses (i.e. negatives effects that affect your current floor occasionally). It also prevents you from being teleported by the Cursed Eye or Cursed Penny when you get hit or collect a coin respectively. After all, they are cursed.
  • The various insects you see — not the enemies you're supposed to kill, but the actual pixel-tiny insects that add to the atmosphere — are interactive. Shoot or step on one and they'll turn into small puddles of blood. If you shoot a fly, tiny pixels of blood will fly off and they'll actually spiral downwards to the floor! If you have the Soul, bugs will be steered away from you.
  • In Afterbirth, the Flush item (which normally has no effect on bosses) instantly kills Dingle, Dangle, and Brownie when used. This also extends to Clog in Repentance, although not Colostomia or Turdlet for some reason.
  • When you defeat Ultra Greed, he turns into a giant gold statue. Midas's Touch will instantly do this, lowering his damage reduction.
  • In Afterbirth†, Glyph of Balance alters the drops of champion enemies so that you'll get what you need the most. If you're almost dead, its first priority is giving you a red heart — unless you have no heart containers, in which case it'll give you a soul heart instead.
  • Plan C kills all enemies in the room, but kills Isaac a few seconds later. This can be used to cheese most final bosses as long as they aren't multi-stage. It also works on Delirium; however, his death animation is so long that it kills the player before you actually get completion credit.
    • Repentance has mitigated this with the addition of the Inner Child item and Soul of Lazarus, both of which revive you in the same room upon death. Additionally, it's very easy to cheese The Beast without any revival items. You can use it at the start of the boss sequence, and all of them will die simultaneously. The downside is that you still die right before the ending plays, so assuming no revival items, you lose your win streak; it'll be set to 0, then 1.
  • Unlocking The Forgotten requires a bomb on the first floor. In case you're playing a character who doesn't start with one and none spawned, using the Sacrifice Room on the first floor will always spawn one bomb as its first reward (as long as you beat the boss within a minute).
  • Afterbirth†'s Secret Character The Forgotten is quite unusual. He uses a bone club instead of ranged tears, which can be swung by tapping the fire button or thrown as a boomerang if it's held. This makes a massive number of items function totally different for him, and the team didn't shy on making sure everything worked. A full list can be read here, but these are a few highlights:
    • Dr. Fetus replaces his boomerang bone with a thrown bomb, which can be cooked by holding it (something the actual Dr. Fetus can't do) but will explode in your face if you charge it too long.
    • Epic Fetus normally replaces your tears with a missile strike. Charging the shot will do the missile strike as normal, but comes with a totally unique animation: The Forgotten holds the missile while you're charging, and tosses it in the air then whacks it with his club when you fire, sending it in an arc instead of the normal straight down. It's totally cosmetic, but amazing to see.
    • Ludovico Technique makes a huge tear follow The Forgotten like a familiar. Instead of controlling it directly, you can hit the tear with a melee attack to launch it. It essentially combines the functions of both the bone and the original item without losing either (albeit this Ludo is a lot harder to aim).
    • Mom's Knife is attached to the end of his bone club, turning it into a Sinister Scythe that deals bonus damage, has more range, and can hit the same enemy twice on one attack. This is functionally a completely different item, which typically replaces your tears with a piercing thrown knife.
    • Lost Contact normally lets you Shoot the Bullet. The Forgotten instead gains an Attack Reflector on his melee hits, not only nullifying shots in an arc, but also launching them back at his enemies.
  • The Ghost Pepper item (and as of Repentance, Bird's Eye) will also create flames whenever Isaac uses an item that makes a fart, like Butter Bean, as well as the Explosive Diarrhea pill. Fitting for a game that revels in Toilet Humor.
    • In addition, using said items with Lilith, who is blindfolded so her familiar fights for her, will still result in her launching the flames herself. After all, only her eyes are forced closed, not her mouth, and that pepper is hot.

     Repentance 
  • The path to Home requires the player to leave the Mom boss room with a teleportation item. To ensure that this can be done on any run, the second floor of Chapter 3 is guaranteed to contain a marked skull that drops a Fool card when destroyed. If you have Little Baggy, an item that prevents cards from spawning, the skull will contain a pre-identified Telepills pill instead, serving the same purpose. The initial version still ran into issues with Little Baggy overwriting the Cracked Key pickup (used to unlock the Tainted characters in Home), but this was fixed.
  • Before Repentance, the Dollar item would only give 99 cents, because that was the coin cap and there was no reason to have it give more than that. However, Repentance changed the item to instead give 100 cents, just like it would in real life. This is only relevant because Repentance changed the Deep Pockets item so that it increased the coin cap to 999. Thus, this change is only noticeable if Deep Pockets is picked up before the Dollar.
  • In Afterbirth†, Glyph of Balance was useless for The Lost. Because of how The Lost works internally, it would replace all champion drops with Soul Hearts. This was fixed in Repentance, making it so that Glyph of Balance never drops health for The Lost, which is really important since it was buffed to also affect room drops.
  • Charm of the Vampire has been around since Rebirth, and turns Isaac into a vampire with the ability to heal red hearts with kills. Repentance also has it remove his reflection in areas where it'd otherwise be visible. It's most apparent in the Downpour and Dross levels, where all the water everywhere makes it very easy to see his reflection.
  • The boss Loki's undead variant is Lokii, two halves of Loki that have been vertically bisected. The Meat Cleaver usually chops enemies into two smaller but otherwise identical copies, but if used on Loki, he turns into Lokii.
    • Similarly, doing the same to The Horny Boys - a fusion of Loki and Hornfel - turns them into their respective parts. This actually makes the battle far easier, because Hornfel becomes a Zero-Effort Boss without the minecart present.
  • Broken Modem will occasionally duplicate room clear rewards, causing the sprite to glitch out before splitting in two. Normally this doesn't work on chests, but it does work if the chests were spawned as an alternate reward by Options?. Repentance also buffed Magneto to automatically open regular and spiked chests within a certain range of the player, which works even during the glitching animation. It turns out that the developers planned for this rare interaction between three specific items, as if you do this while on the Chest or Dark Room, where all chests are guaranteed to spawn items, then the chest will contain a glitched item from TMTRAINER.
  • Introduced in Patch 1.7.9b, if you somehow have the Glowing Hourglass on hand in the starting room of a run (whether through debugging, Eden, or a Game Mod like Auri) and immediately use it, you'll immediately warp to Home, due to rewinding time to before Isaac flees into the basement.
  • Dream Catcher is a passive item that changes the floor transition nightmares to instead show Isaac finding the item that will be in the next treasure room, as well as the upcoming boss. However, there is a very rare treasure room layout that contains no item, but instead a poop and some pickups. If this happens to be the upcoming treasure room while holding Dream Catcher, the animation is changed slightly to show Isaac falling to his knees in agony at the disappointing contents of the room.

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