What does “it took one away” mean in the line, “For each superpower his brain gave him, it took one away” in encountering a gun attack?

Solution 1:

There's no doubt that it here refers to his brain.

It's semantically confusing, because we have to bear in mind that his brain is being treated as something different/external to him. But structurally it's the same as...

For each door God closes, He opens another. (the number of "open doors" remains constant).

The "redundant" version of the key sentence in OP's text would thus be...

But for each superpower his brain gave him, his brain took another superpower away.

To be honest, I don't think native speakers would normally have a problem identifying the referents of it and one (unless perhaps the him/his brain distinction was causing confusion already).