You can start the following Robot Wars missions when you're done with the Hack Teh World Main Operation. We'd recommend you unlock the Robot Hacking and Security System Shutdown research upgrades before embarking on this set of missions.
Drop the Baby, Like Minds
When you arrive at the facility head towards the water, dive in, and swim across to the dock. Take out the solitary guard and then tuck yourself out of sight somewhere near the main building.
Deploy the Jumper, open the gates, and move up the ramp to the left, disabling the patrolling robot if you can. Head through the vent and climb the stairs off to the left, follow the walkway around, and jump across the platforms towards the security gate ahead. Open the door on the left and use the Jumper to unlock the doors, then recall it.
Follow the same route on foot and collect the EMP part from the office then leave through the other door. Descend the ladder and grab the EMP part from this room, either timing it to avoid the robots or disabling them if you can. Head back up the ladder and exit the building through an upper door towards the last marker.
Avoid the patrolling guards and robots as you collect the last piece, and then enter the office to unlock the doors for Wrench, then when the robot is in place enter the storage warehouse and plant the bomb on him.
When you have control of Jr, open the warehouse door and onto the stationary conveyor belt. Keep going until you reach an impasse then hack the camera above and to the left of you to find a switch.
Open the shutter and return to Jr, continue along the conveyor until you reach another dead end, then use the nearby switch to rotate the platform. The next obstacle is a lift followed by another rotating platform and a shutter, both of which are operated by the same switch. Finally hoist yourself up on the lift, drop off the end, and fulfil your destiny in the server room.
Man vs. Machine
Enter the Tidis building and head for the marker - there are a few robots and guards here but avoiding them isn't too taxing, but being able to shut off security gates will be a major help. Once you reached the locked door use NetHack to locate the panel, disable it, and rejoin the trail.
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Hack the server then head up to the fifth floor and hitch a ride in the elevator. Once in the vault hack the panel on the right to trigger a switch puzzle:
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Activate the super awesome robot spider and use it to shoot out the fire suppression points on the walls and ceiling - the ones above will require you to climb up the wall to get an angle on them - as well as laying waste to the guards.
When the doors open head through each one in turn and destroy the prototypes within then head for the lift shaft. Climb up the walls to reach the power room and shoot out all the equipment inside to shut down the system.