Drop the Baby
Talk to Wrench in his garage to start the cutscene.
Head for the facility with Wrench. When you get there, go right and climb up the ladder to get onto the roof of the building opposite from where the objective is. Settle yourself behind some cover and drop the Jumper. Head over the side of the building and go for the first piece of the bomb, distracting or shutting down any guards or robots in your way. As a side note, you can also hit the bots with the love hack to sow some chaos instead, whatever works for you.
Once you have that, head along to the vent in the side of the building and go inside. \go upstairs to the control room to get the second part and also to hack the laptop for the access code.
Exit this room and go through the laser gate to reach the room with the final piece of the EMP. Hop down, grab the part then recall the Jumper.
There’s a robot on the other side you can shut down or otherwise hack to get out of your way whilst you hack the doors.
When that’s done, recall the Jumper once again and climb back down the ladder to the street. Go to the garages and use the access code to unlock the door closest to Junior. Get inside and install the EMP on him. When that’s done, leave the area to complete.
Meet Ray and watch the cutscene.
Man vs Machine
Go to the Tidis entrance and activate the marker to start the mission. You’ll be in control of Junior for the first part.
Get yourself onto the track and follow it until you are stopped by a gate, activate NetHack and jump into the camera nearby to get a view of a switch, throw it to open the gate barring your way and head on through. Keep following the track until you’re once again stopped, use the camera behind you to hit the turntable switch to get you onto the right path. Head through and use the next switch to lower the lift with you on it.
In the next room follow the same routine with the turntable, then when you get to the lift, look to your right to hit the switch. Drive off the ledge, go to the server room and set off the EMP.
Head into the Tidus building and distract/shutdown and/or stun/shoot your way up to the objective marker. There aren’t too many guards here so if you keep a good pace up you should be able to get through without being spotted. Once you get to the room beside the objective, you’ll need to hack the terminal in the next room to unlock the door. Get yourself in cover and send the Jumper to do the job.
Once it’s unlocked, head on through to the server room but not before you trap the transformer box on the floor to stop any unwanted interruptions. Once the hack is complete, sneak out of the server room and up the stairs to the CEO’s office. Make sure you disable the motion sensor before you go through the door though. When you get to the office, watch for patrolling guards then ride the elevator down.
Take control of it and turn up your music of choice, it’s time to wreck Tidis’ day.
Next is the backup server’s power supply. Climb up the walls of the lift shafts until you get to the room, then just hold down the trigger and go full Rambo on that place. When it’s in ashes, your operation is complete.