Cloak & Daggers

Cloak & Daggers is an optional side quest in Deus Ex: Human Revolution, and has a similarly named achievement/trophy for completing it.

Jenny Alexander, an undercover cop and a friend of Adam Jensen's from the Detroit police force, is investigating a police officer named Jack O'Malley, suspected of corruption, and could use Jensen's help. She is found in the Detroit streets, near the entrance to Derelict Row, undercover with a group of prostitutes.

Overview

Alexander requires four things from Jensen to lock down this case:

Incriminating evidence that O'Malley is hiring hitmen to kill figures that could cause problems for him. Jensen must meet with O'Malley and pose as a hitman.
Once Jensen has received his orders from O'Malley, Jensen must prep O'Malley's new target for retrieval by the Detroit Police.
Incriminating evidence that O'Malley is corrupt. Jensen must investigate O'Malley's apartment and search for any evidence that could help in the case against O'Malley.
Incriminating evidence that the Derelict Row Ballers are being supplied illegal weaponry. Jensen must infiltrate DRB territory and find the incriminating weapons shipment.

While not necessary to complete the quest, Jensen can also recover a weapon that was used in a previous hit ordered by O'Malley. Staying hidden while in DRB territory will also aid Alexander's case.

If one goes to the Police Station, Alexander's office is on the third floor, code 3727. On her wall, there is intel on Derelict Row: photographs pinpointing certain key enemies, loot stashes, and entry points.

Walkthrough

The Hit

O'Malley is located in the alley beside the Detroit Police Station. Jensen must meet him there and pose as the hitman to receive his assignments. O'Malley will be suspicious of Jensen, partly recognizing him as a former police officer, but by playing the part of the consummate professional Jensen can throw him off the track. O'Malley orders Jensen to retrieve the murder weapon from an alley, then use it to kill a Motor City Banger named Double-T, then plant the weapon to incite a gang war between the Bangers and the Ballers.

If the player has the C.A.S.I.E. Social Enhancer augmentation, O'Malley can be appeased (He is an Alpha type personality.) to give a 1000 "advance" on the hitman job.

The weapon, actually a Crossbow, can be found in the side alley entrance to Derelict Row.

The Banger

Jensen's target, Double-T, can be found in one of the apartment complexes, the same one Seurat is in, on the third floor. The complex can be entered through the windows. He is guarded by five other Bangers, armed with shotguns and machine pistols.

One Banger is outside guarding the hallway and is friendly, merely telling Jensen to piss off when he approaches. Three Bangers are in the living room - two watching the television, and one patrolling. The last bodyguard is with Double-T, in the bedroom. The bedroom door is locked with a level 3 terminal, but the code can be found on the Banger in the hallway (the code is 3733). Alternatively, one can enter the room from outside the hallway, by punching out a weakened wall. If you cannot get through either of these ways, fire a round from a non-silenced weapon directly outside the door and Double-T and the banger with him will open the door to look for you.

Alexander wants Jensen to take Double-T alive - the stun gun is ideal for this. The other Bangers can be taken out with a nonlethal approach fairly easily as well - both the Banger in the hallway and the patrolling Banger can be taken out with melee takedowns, while the pair in the living room can be shot down with the tranquilizer rifle. The final bodyguard can be shot down from behind cover with the stun gun. Alternatively, everybody can be taken out with a single P.E.P.S. blast or Gas mine if lured into the hallway. (Warning: If the Banger that gives the warning cutscene is shot with stun gun, or Tranq regardless, it will result in a death, voiding Pacifist.)

Various loot can be found in Double-T's apartment. This can be quite lucrative because there is a weapons dealer down the stairs. Instead of picking up all of the weapons at once (which converts them into ammunition), pick them up one at a time then carry them downstairs for a nice tidy profit. (example: One shotgun = 750 , shotgun ammo = 50 or less) This can help if the player is having trouble getting the praxis software from the LIMB clinic.

O'Malley's Apartment

O'Malley's apartment can be found in the same complex as Brian Tindall's. Although the apartment door only has a level 2 terminal, the bedroom door has a level 4 terminal, and the necessary evidence is located within the bedroom. Bedroom code is 1029.

NOTE: Instead of hacking the outside gate, the player can stack a crate on top of the dumpster next to it to gain access to the apartment complex from the fire escape, or use the gate code 0002.

NOTE: Inside his apartment, there is a pocket secretary on the bottom shelf, across from his desk and next to a plant, that contains the security code to the bedroom.

NOTE: Inside his bedroom, there is a safe beside the computer with a level 3 terminal. The safe's code is 1031.

The evidence required is a shipment of drugs in O'Malley's bedroom. Picking it up will complete this portion of the quest, but you can also find a weapon case on his bed and more evidence can be found on his computer. A large quantity of loot can be found in the bedroom. The bedroom is rigged with several frag mines. One of them has a large box in front of it - attempting to pick up the box will immediately detonate the mine, killing the player. Crouch-walking and manually disarming the mines will allow Jensen to retrieve them, or the player can manually detonate them by shooting them from afar. Another method would be to quickly run part way into the room, and then sprinting back out before the detonation kills Jensen. A third method is throwing one of the boxes from outside the bedroom inside. This will detonate all the mines with no risk or ammo loss.

The Weapons Shipment

Jensen must infiltrate Derelict Row to find the incriminating weapons shipment. Upon entering the actual complex and thus entering Derelict Row Baller territory, all Ballers encountered by the player will be hostile. Getting seen will also fail the optional portion of this sidequest.

NOTE: If you kill and/or knock out all the enemies in the area BEFORE receiving this quest, completing the side objective of not being seen will be trivial.

The shipment is located under the flooring in one of the north-eastern buildings, on level 1 though that area is not indicated on the map., It can be reached either through crawling under the crawlspace, the sewers, or through a nearby door. Aside from the shipment itself, the crawlspace also has several weapons, frag grenades, and a weapons upgrade.

Hidden on the wall here is the famous Dopefish.

Conclusion

Upon completing these four objectives, the player should meet with Alexander again to report their progress. Handing over the crossbow to Alexander, taking down Double-T alive, and having found the weapons shipment without ever being seen by the Ballers will complete the optional portions of this quest. If the player chooses not to give the crossbow in, the player will not receive the weapons upgrade but will still complete the quest. (If you mod the crossbow during this quest handing it over will not be possible) Alexander then prepares to make the final arrest. Jensen can either have her do it, or do it himself.

NOTE: If Jensen declines the final arrest option, Jenny will actually give Jensen a repeat mission reward of both credits and the weapon mod if he handed over the crossbow murder weapon to her as well. (Confirmed) This second bonus reward may be a glitch in the game as the action could be getting read as a secondary unintentional end of mission trigger, whereas doing the extra work and taking O'Malley down personally does not net you anything other than completion of the mission story arc and the normal end of mission reward of one mod and 1000 you would have already received when turning in the evidence including the crossbow murder weapon and a slightly different ending comment from Jenny.

NOTE: If Jensen declines the final arrest option but does hand the crossbow over, he can kill or knock Jenny out to take the crossbow back after the quest rewards are given. Otherwise, if Jensen arrests O'Malley himself, Jenny will not carry the crossbow anymore.

If the player opts to have Jensen arrest O'Malley, he can be found in his apartment. He will attempt to bribe Jensen with an "enviable amout of money" (3000 ) - Jensen can either let him go (and receive The Take achievement after talking to Jenny Alexander again), or decline, in which case O'Malley will pull out a pistol and try to kill him. Taking him alive is preferable for completing this quest - again, the stun gun or a quick punch is ideal for this. You do not even need to speak with O'Malley, and can simply walk around his desk and take him down. Speaking to him, however, nets you 300 points for 'Completionist' versus the 100 for simply dropping him.

Glitches

Many players have had the patrolling MCB member who should be in the kitchen, spawn outside of the playable area. Reports claim that going to LIMB, or your apartment to force a reload will get him to respawn back inside the playable area, but this has not worked for some people. If doing a pacifist run, dragging all of the unconscious members into the bedroom has succeeded in spawning him as well. There is no known reliable fix for this glitch so far. If this happens, you cannot complete the quest, Alexander will act like the mission is not complete. Touching Double-T in anyway will kill him and the quest will fail.
One way of possibly finishing the quest is to alert the patrolling member outside by shooting at the watertower with a weapon. If any luck, the member will eventually be seen on the edge of the water tower floating on nothing and can be killed.
If the player experiences this glitch, go to the highest part of the fire escape outside of the apartment with the MCB gang members in it, and jump up and down on the railing in order to get a clear shot. Make sure you turn on Objective Locator (Options>Gamplay>Objective Locator>On) and it probably would not hurt to turn on Aim Assist. You should see the enemy indicator near the adjacent water tower. Pull out a gun and aim it at the indicator. Even if the enemy cannot be seen, your reticle should light up, meaning he can be shot. The best way to do this is with the tranquilizer gun (scoped). Remember the darts arc, so line up the so that the Objective Locator is at the bottom of your scope. It may take a few adjustments to how high you are aiming A Sniper Rifle will also reach him, also the pistol, but the Combat Rifle will not. Aim directly at the center of the indicator and fire, and it should render the guard unconscious. Sometimes he is not near the upper area, in which case you should try to get as close as possible to the indicator for this to work.
If the MCB member is outside of the playable area, sometimes he will be patrolling. The indicator will be seen moving if this is the case. If the player waits long enough, sometimes the enemy will drop down and end up inside the room he is supposed to be in, and you can proceed normally.
If the guard is outside the playable area, and not visible, another way to kill him is to throw a grenade, although concussion grenades do not seem to work, and it will make P-Gee and Bee-K (who are nearby, unless you already dealt with them) hostile.
Another glitch on this quest is the fact that after you retrieved all the evidence and got Double-T knocked out, and the only thing left to do is return to Jenny, if you try returning to her through the shortcut located by the apartments (the hole in the fence near P-Gee and Bee-K), you will automatically fail the quest once you get close to the fence. Jenny disappears at this time and can no longer be found in the game. You must take the alternate route to Jenny to reach her without her disappearing. This fence glitch will also cause you to fail the mission at any point, but Jenny will not disappear.
Hacking the computer in Double-T's room might also make the guard appear in the kitchen.

Possible solutions

Get close enough to the MCB hideout to trigger the quest (all the blue crosses appear). Then do not do anything else except turn round and leave. Take the shortcut back through to Jenny's side of the map and take the long route round and come back in past the abandoned gas station. After you have got back up to the MCB hideout again you should find that the glitched gang member is now in the kitchen where he is supposed to be.
The MCB member who spawns outside is likely stuck in the ceiling or the wall right outside of the apartment if not visible to the player. There is a point in the wall that is not completely solid, however, the player can not pass through this part. Getting the MCB member out is reliant on getting his attention through use of unsuppresed weaponry and luck. The video below shows where exactly the MCB member gets stuck, and this possible solution.
After trying all the solutions in this guide to get the MCB member to pop outside of the wall, (shooting inside the hideout to draw his attention, or going out onto the fire escape ledge to shoot at the blue marker with a sniper rifle) Try entering your home apartment and coming back out again. This may work as a final solution.
Saving right next to the entrance to the apartment (even after having taken care of everyone but the phantom MCB member), and then reloading this save can make the phantom MCB member reappear in the kitchen shortly afterwards, but also has a chance not to work.
Go to Seurat on the lower floor and sell him something then go back to the stairs leading up and the MCB member will be at the top of the stairs. This solution is confirmed to work on PS3, but other platforms are unconfirmed.
Going down past the basketball court and into the little crawlspace (which either leads to the police or your apartment building) and exiting the vent on either of these exits will make the objective indicator change location (indicating a change of position of the MCB member). To have him stay in the 'new' position, exit via the far-end of the vent-system and then walk ALL the way around the map: through the railway-station, past the gas station and back to the basketball court. This worked on PC when other solutions failed. Now, the gang member may be either close to the water tower, on about the same level of height as the highest staircase level (allowing for the other solutions posted which MIGHT affect pacifist) OR he might be directly above the kitchen in the apartment room (allowing for an unsilenced shot to alarm him and get him to fall into the kitchen). If neither seems to be the case, try again: go through the vents again and watch for the objective indicator to change location as you emerge. Go through the station again, to make sure the guy stays in his new place.

Video Guide

The following guide will help you infiltrate Derelict Row without being detected AND without killing anyone -- Pacifist approved!