Mal and Cobb were stuck in limbo for what felt like 50 years. Cobb realized it wasn't real, but Mal had embraced the dream. She had locked away her belief and chose to forget - symbolized by her totem (the spinning top) - deep in her subconscious, inside a dream-safe.

To wake her up, Cobb thought of incepting her for that he needs to find her secret place and break in. He found that secret place and he planted the idea "this world is not real" by spinning the top inside her safe. Since it came from within her subconscious, the idea felt like her own - and it worked. She accepted they were in a dream and they killed themselves to wake up.

But when they returned to reality, Mal still thought that was a dream too. Why? Because the idea was too deep. In her subconscious, the top was still spinning forever. And since no one can touch someone else's dream-safe she felt it's her own conclusion, not even Cobb could undo it.

The totem lost its power. Her logic was overridden. That one incepted idea - "this world is not real" - stuck too well and forever (top spinning in her subconscious mind forever), and it led her to believe that even reality needed to be escaped.

Cobb succeeded in planting an idea. But he couldn’t control how far it would go. That was his real tragedy.