In Act II, you will complete a mission called "One Foot in the Grave." After you do that, you'll receive a call from a character named Tobias, who wants you to find weapons crates around the city of Chicago. If you find all of them, you can obtain a silenced Goblin weapon and an achievement. Though you can search for the crates ahead of that phone call, you'll have things easier if you wait until after Tobias makes his request. That's also a requirement before you can complete the mission that ends the investigation.
To complete the investigation, you'll need to look for the icons on the map (unlocked by clearing ctOS towers) and then . You can find the crates in any order that suits you. I'm providing general instructions to find each crate below, by region, with screens showing the location on the map and the location of the door you have to enter to find the crate.
Near the northwest portion of Mad Mile, not terribly far south of the hideout in that vicinity, you'll find a crate. It is hidden around the back side of a large building. The camera that points toward the security lock is on a building across the street. You can point to the lock on the roof and scan it to unlock the door, then head around behind the building on the ground level to find the crate and an Audio Log.
Look on the large island near the western side of the Mad Mile region. There is a large building with "Sweet & Spice Thai" signs on its face. If you head around to the side, you'll find a locked door. Continue around back behind the building to find a ladder to a low rooftop. There, you can see a sloped ledge leading up to another roof. It's possible to climb onto that sloped ledge, from the side (not the front) and onto the roof. Then you can drop around into the fenced area on the rooftop and scan a lock from close at hand, rather than a distant camera. That unlocks the door you saw earlier, so you can enter the room for another crate.
Near the north central side of The Loop region, you'll find a crate behind a locked door that is in the underground tunnel. Head down the stairs from the street and you'll need to follow a white line while your Profiler is open, to reach a stack of wood pallets at th eedge of a fenced area. There's a panel on the wall behind them that you can scan to unlock the door. Then head over to the door where it is indicated on your map (diagonally, it's across the tunnel) and pass through it to find an Audio Log and a crate.
Near the south side of The Loop, a short distance southwest from a hideout in that vicinity, you can find a locked door in a dimly lit junction between a bunch of high buildings. Just over the bay door you can use to access the room, there's a high camera on the wall that points toward a ledge where the security panel waits. Scan the panel, then enter either the normal or the bay door to enter the room and find a crate and Audio Log.
Near the far west side of The Loop, east of where the long bridge joins that region with Parker Square, you can find a locked door southwest of the nearby hideout. Head back down the street to where the buildings meet with another street, at an intersection. One of the buildings across from the side of the street with the building you wish to enter has a camera positioned on its side. Hack into that camera and look toward the right, along the raised area. You'll see the switch console you need to unlock. Then head back down the alley to reach and open the door. In the room, you'll find an Audio Log and more weapons.
Along the north side of the Brandon Docks region, off to the side of the main road leading north into The Loop, you'll find a locked door on the other side of a brown mesh fence along the marina docks. Hop the fence and look along that building, between a container and a pile of wood paletts. There's a switch console. Scan it, then head around the building and enter the door to find a crate.
The Wards extend fairly far east into the middle portion of the Brandon Docks area. Look for the point on the map where The Wards extend furthest east, then from there look a short distance northeast on the map to find another locked door on the building behind Jay's Garage, not far from a bridge. From that door, trace the wire around the building to the left and over to another building. Run along that building and up to a higher area with steps that lead to an overhead fenced walkway. Proceed along that walkway to in the direction from which you just came to find the switch console that will unlock the door. Then backtrack and enter that door to discover a crate and an Audio Log.
At the north side of The Wards, look for the Jay's Garage building. There's a camera mounted on the corner, to the upper right of the locked door. Hop the fence below that camera, then head down the alley between two buildings and swing a right at the end. You'll find a ladder on that building's wall. Climb it to the roof. Then head around the roof and climb to a higher portion. Walk around that narrow ledge to the back side of a brick structure to find the switch console. Then backtrack and open the formerly locked door to find a crate and an Audio Log.
Along the southeast corner of the Parker Square region, you can find a locked door along a back side of the West Side Auto building. Cross the street to the building advertising live music. There's another building off to the side from there, with a camera mounted on the side. Hack into the camera and look out at the building ahead of it to see the switch console on the roof, which you can unlock remotely. Now head back to the locked door and enter it to find an Audio Log and a crate.
Once you have found the crates, you'll gain access to a new bonus mission. It is located near the north side of the Brandon Docks area, not far southwest from the local hideout. Accept the investigation mission, but be ready for a challenge because you have to start over if you're killed partway through it.
Reach the Fixer warehouse.
You need to infiltrate a Fixer warehouse, and the enemies are heavily armed. You'll start by finding your way inside their base, but you can get a head start by killing everyone before you even properly arrive.
From where you start the mission, head forward and climb some metal stairs to the top. There is cover along an elevated metal balcony, and from it you can see out to a camera positioned on what looks like a water silo. Hack into that camera.
The camera provides a view of another camera on a pole to the right, so travel to that one next. It looks out toward guards on ledges to the left and right, and another camera to the left. That particular camera gives you a good idea of where everyone is located. You can see them patrolling.
It's possible to take out all of the enemies from your current position, if you brought a sniper rifle. You can start by using any explosive points on the map, and any explosives the guards carry. Then take out any stragglers with the sniper rifle. When the area is cleared, you'll receive a new objective.
Prepare for enemy reinforcements.
You can run down and set up IEDs and such during this phase of the infiltration, if you wish. There's nowhere near enough time to do much of anything useful, though, so you might just want to stay where you are.
Eliminate the fixers.
From the high scaffolding, you can throw frag grenades at the areas where you see tire tracks, which is where enemies will pull up in vehicles soon.
There will be plenty of Fixers that get away from their vehicles and come searching for you, also, unless you're a genius with frag grenades. You can try hacking into cameras and using the environment to eliminate them, but it's important not to get distracted and leave Aiden exposed to a flank maneuver. Ducking behind cover and gunning them down one at a time may be the safest approach.
Prepare for enemy reinforcements.
After that first wave of reinforcements, a second one will also come.
Eliminate the Fixer bosses.
You have to take out the last of the Fixers in the area now. There will be a few heavily armored Elite enemies among group, so hopefully you have the ability to use Takedown moves on them (it's unlocked on the Skill Wheel) and can expedite the fight. The Elites also are no good around explosives, so that can also help. Once you clear out this final wave, the mission concludes and you receive your achievement/trophy reward.