That's what Cobb's inception was: that her reality isn't real. He did it in limbo, and it spread in reality. Whatever he did in reality couldn't get rid of his virus idea that took over her.

I'm so glad someone has jumped in with an answer to my conundrum. But sorry, I still must be missing something...maybe you can clarify. When you say that Cobb convinced Mal that her "reality isn't real", wasn't that inception illustrated in the film by Cobb breaking into her limbo safe and spinning the top? Don't we presume that she came back later and saw it spinning, and therefore agreed to leave limbo? Or are you suggesting that Cobb removed her trust in the totem cometely? Because if that's the case, how do we make sense of the mini montage of images we see as Cobb is telling that story?

"Don't we presume that she came back later and saw it spinning, and therefore agreed to leave limbo?"

No you can't think of it that way. Their safe is basically their mind and ideas. She doesn't have to literally go into the safe and see it spinning. Cobb going into her safe and spinning the totem was basically him putting a thought into Mal's mind, the thought being this place isn't reality. But when Mal goes back into the real world, she still thinks the totem is spinning, meaning the only way to leave this other limbo (the real world) is to die.

This is just my ideas, not sure if it's right or wrong.

Yeah, I think you're mistaken there. Notice how Fisher had to go all the way into the vault for the inception to take hold. Same for Mal. BUT...GOOD NEWS...Misanthrope86 has wisely suggested that although she probably saw the totem, when she returned to the real world, the idea that was planted so deep in her subconscious became more powerful than her trust in the totem. The top therefore become irrelevant basically.

Mal's totem wasn't a tangible thing; it was a thought.

i think you've been mixed up buddy. Cobb says very plainly that Mal's totem was the top, and that he adopted it after her death. after talking withe misanthrope86 for awhile about this question, however, i'm pretty satisfied that her response (see the "answers" section) is both sound and helpful. check it out if ya feel like it.