After shocking the initial rebel with the ID10 unit, you have to activate two terminals to access the ventilation. So, the fastest way to do so, is head directly to the right and activate bother terminals and head for the ventilation. Once inside it is fairly simple, and if you sprint you can get through the shock areas with only one hit to you (not fatal) so go ahead and run through it. After that, you are dropped off into a hallway, if you sprint, take the corner sharp and stay low to the ground, you can actually get under the door before it closes. The guards might kill you but it is a risk. After that you head to the next ventilation area. Once inside go through the first one like normal, but once the vents bend upward you should look straight and use jump (SPACE by default) to go up to the next vent opening. It is interesting to note that the droids' upwards and downward motion is much faster than its forward or backward motion, thus making it more worthwhile to look straight and use jump, rather than point to where you are heading and move forward. Once outside the vent, head for the terminal to remove the lockdown and head to the vent and head to Iden Versio.

After Iden says "...I will signal for extraction", you are able to use the ID10 to open the door. Once that has been done, you can sprint to the next door past the guards and immediately use the ID10 to open the door (guard take down optional ;) ). After that you have to run and grab the weapon and open the door as fast as possible. Now for the next area, you HAVE to kill all those who are in the next area, otherwise you can't delete the intercepted message. So you can kill the inital three, use the ID10 to open the next door, while he is busy doing so, kill the two annoying rebels that always kill my runs on the walkway. Then run inside, activate the door, knock off the other three rebels while the ID10 is busy, then knock off the one inside and bingo you can do so.
After deleting the message, you have to grab a gun, then you can open the door. You can run past and ignore all the rebels in the area, once as you get to the next door, use the ID10 on the door, wait a second, then shoot the door behind you (if you don't wait a second or wait too long, the door opening can take 10+ seconds longer). Run through all the areas as fast as possible ignoring as many rebels as possible, make it alive to the next door, use the ID10 ASAP, kill off any rebels, wait for the door to open, sprint to the finish, then congrats! You have officially made a decent run of The Cleaner.

Possible Time Saves? Find way to glitch through barrier in lockdown. Find way to get past annoying 27 second opening door before Iden makes it to the escape pod. Someone please find a way to skip the dialogue.