Assuming that you have completed all Prototype 2 //Blacknet sets, up to this point, finishing Operation: Clockwork is the only way to unlock a new achievement/trophy named //BLACKNET Hacker.
Operation: Clockwork, just like the previous mission, is unlocked after you finish Last Resort.
To begin Operation: Clockwork find and access Terminal 12 in eastern Midtown (Coordinates: 761, 226).
Operation: Clockwork is divided in three sub-missions, and the first one you will have to complete is Gentek Support 15-G.
This specific part requires the memories of Dr. Alexander Murray. You will find him in a small park south west from Terminal 12 (Approx. Map Coordinates: 677, 295). Consume him to update Gentek Support 15-G.
Note: While hunting for Dr. Alexander Murray, you should also check the high building near the park where you find him (Coordinates: 683, 267). If you climb it, you will unlock the Icarus achievement/trophy for reaching the highest point in the world. In other words, the highest building in Prototype 2 is in Midtown (Red Zone) and its approximate map coordinates are: 683, 267. Look for the black smoke coming from the roof.
After you consume Dr. Alexander Murray, go to the small Blackwatch base in Western Chinatown and hijack the helicopter you find there. Using the helicopter kidnap the scientists marked on your map by landing on top of the buildings and on the ground.
Tip: While flying the helicopter you will be attacked by Flyers. At this point you flying skills will be tested. Try to avoid the Flyers and dont take damage, if you wish to earn more experience points.
The second scientist and the third are well protected by Hydras, so make sure you avoid the rocks they throw at you, by pressing Y.
After you clear the area where the Templar scientist is located, fly back to the base in Chinatown and keep RT pulled, on your way back. When you reach the maximum altitude, press B to eject the helicopter and watch the scientists dying.
Now, return to Terminal 12 to access the records of Cpl. Kevin Duke. You will find him in a small base in eastern Midtown (Map Coordinates: 767, 306) Consume him to unlock the second phase of the mission, named Infected Salvage 8-D.
Now, go to the Containment Site (569, 368) to see the Goliath captured by Blackwatch. Unfortunately, you also have to kill it, but this is not the first Goliath you encountered so far, so the strategy remains the same.
Its members are the weak spots, however dont forget that since your last fight against a Goliath, you have unlocked some new weapons, and one of them is the Whipfist. Your Brawlers can also keep the Goliath distracted. After you defeat the Goliath return to Terminal 12 and access it for the third time.
Elwood Pine is your final hunting target in this mission, and you should look for him NE from your current position (Approx. Coordinates: 639,234). Be careful because the Evolved doctor wont give up without a fight. Consume him too and you will unlock Infected Salvage 8-A.
For this part go to the western base in Midtown (Coordinates: 515, 281) to locate and kill Mercers Infected specimens.
To enter the facility, first consume the commander on the roof, and then get inside using the hand scanner. Now, approach the console on the first floor, and release the Infected. Wait until they kill the guards, then go downstairs and kill all of them. Go back and activate the console to release a new wave of Infected.
Take them out too, and then exit the Gentek facility to finish the mission and earn the correspondent achievement/trophy.