Let her know somenone knows.

You continue watching Miranda or Shepard or whoever, It's confusing, and wait until she leaves the apartment to make your move. You decide to start small. As such you leave a copy of the recording you made on her computer with a message saying that she has to tell you how the situation you recorded came to be, how to do that, and to await further instructions.

As you promised not to tell the Alliance, Cerberus, Aria or post it on the extranet for everyone to find as long as she followed instructions you wait two days before checking if 'Miranda' listened to you. Somehow she did and the explanation is incredible. To be honest you don't understand her explanation at all, but then you are not a genius Cerberus scientist.

Apparently some time after defeating Harbringer Shepard died, this was when her team scattered, and some time later her body was brought to Cerberus to be brought back to life. This took about two years and an insane amount of money to do and was overseen by Miranda. But even after two years they managed to create a living body from a few cells that couldn't wake up. The resurrected Shepard was in a coma. Eventually Miranda used some kind of virtual reality thing to go into Shepard's brain and 'wake up' her mind. This went wrong and Shepard's mind went into Miranda's body while hers got stuck in Shepard's. Yeah, weird, sciency and metaphysical.

Luckily on top of the impossible to understand stuff she also included a few anecdotes on what happened shortly after. One anecdote is about how the two of them explore their new bodies together in the showers, another is about how they try to fit into their new lives (apparently they communicate with each other), and even one about the two of them about the two of them discussing possible mental changes(apparently they became a bit paranoid about that when they thought they were behaving weirdly).