We didn't see it happen, which at least to me raises a conspiracy flag, but Jensen, Sarif et al seem pretty sure she's corked it.
She was killed during the attack, we're told. Conspicuously absent, however, is Jensen's erstwhile love Dr Megan Reed. Jensen's back on his feet (though they're probably not his original feet) and so, apparently, is Sarif Industries. Now, where did we leave things? Last time on Deus Ex Street, poor Adam had been beaten senseless then strapped to an operating table to have most of his internal organs and limbs replaced, nice Dr Megan had gone missing and those naughty geezers from the other side of town had been causing all kinds of problems for friendly neighbourhood science genius David Sarif.