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The story is told in a crayon-drawn opening. Isaac's mother hears a voice from above telling her to strip her son of everything corrupt, then his toys, then his life. Isaac flees through a trapdoor into the basement, and the game begins. Every run drops you into a grid of rooms, one screen each, that you clear by firing tears at whatever lives there: flies, gapers, leeches, and a rotating cast of bosses drawn from McMillen's sketchbook. Find the boss room, beat it, take the trapdoor down. Eight floors later, on the second stage of the Womb, you face Mom, and the endings start to branch depending on what you have unlocked.
The reason a fifteen-minute run stays interesting after a hundred attempts is the item pool. Every floor has an item room and a shop, and each pickup permanently changes Isaac for that run: a bigger tear, a faster tear, tears that home or split or set enemies on fire, a knife instead of tears, wings, a laser from the eyes. Effects stack, so a run built from ten random passives can be a nonsense combination that is either useless or breaks the game in half. Pills are unidentified until you swallow one, tarot cards give one-shot effects, and bombs open the secret rooms hidden between the ones you can see. Health comes as red hearts you can heal and soul hearts you cannot, and the balance between them is a constant negotiation with the devil rooms, which sell items for heart containers.
Progress across runs comes from unlocks. Beating Mom for the first time opens further floors, meeting certain conditions unlocks the alternate characters, each of them a tweak on Isaac's stats and starting item: Magdalene with more health, Cain with a lucky foot, Judas with high damage and one heart, Eve, and a hidden character who starts with no red health at all. In May 2012 the Wrath of the Lamb expansion added floors, bosses and hundreds of items, and it was the last thing the Flash engine could take; McMillen has said the technical ceiling of Flash is why the game was rebuilt from scratch with Nicalis as Rebirth in November 2014.
The 2011 Flash version has quirks the remake sanded off. Tears travel in the direction you press, with no controller support in the original, so aiming is the four arrow keys. Big rooms can drop the frame rate, the drawn art is flatter and more hand-made, and the difficulty curve is meaner because balance passes came later. Some people consider it the better game for exactly that reason: it feels like a sketch rather than a product. It suits players who want the roots of the roguelike boom that followed and who enjoy figuring out item effects by getting killed by them. Nintendo refused a 3DS port in 2012 over its religious content, which tells you something about the tone.
On LemonArcade it runs free in the browser with no download or account. Flash itself is dead, so the game runs through a browser emulator, which is why it is a desktop title here: you need the keyboard, and a phone screen gives you neither the keys nor the pixel clarity. A run takes ten to twenty-five minutes, a fresh run starts instantly, and the early floors are a fair test while the later ones are a wall. Whether unlocks persist depends on the emulator keeping its local save, so treat character unlocks as a bonus rather than a guarantee.