The Missing Link covers the timespan in the main game between Stowing Away and Rescuing Megan and Her Team. You were detected hiding in the stasis pod and were ultimately retrieved for interrogation after a heated battle. When the DLC starts, you are being interrogated by Pieter Burke and Netanya Keitner. You've been stripped of your gear and upgrades, so it's back to square one.
If you kill or knock out enemies in "Stowing Away" prior to this detour, or before "Tong's Rescue" involving Tong's son (either downloaded or packaged in Director's Cut), they will comment on the kind of person you are. Also, your talk with Keitner will determine the gun layout. As a nod to "Deus Ex", your actions determines the outcome throughout this detour. Your choices are mainly stealthy or going out with all guns blazing.
Escape and find your equipment[edit]
Suddenly you will be free from the EMP generator chair and you can leave your cell. Beyond the outer walls are two guards conversing, and you'll see locked door with a level 1 security panel on it. It leads out into the open, so a better plan may be to move the crate and use the vent cover underneath. This takes you under the floor to a passage on the other side of the room. From there, use the east corridor to move north up the passageway, crossing the first intersection when the roving guard is on the other side. In the next room after the intersection, get cover behind the crates and wait for the two soldiers to finish their conversation.
When they walk away, go through the first door on the right, then hop over the crates and you'll see another vent cover above the mahjong table. Use it to cross to the next room where you'll hear another conversation. When the guy with his back to you next to the vent walks out of the room, follow him out and take a right around the corner when he goes left. If the stationary guard isn't facing the control panel for some reason or you want to take them out, take out the guard in the hall when he's at the end where you came in, then get the guy in the room. Through the next door, you'll be in an empty passage running east-west. When you hop the crates, jump up to the pipes on your right for a traveler bonus and a pocket secretary with some codes on it. Around the corner is a level 1 security door you can hack or use the code on, and it leads to the passage with the ladder you can take up to the next deck.
As soon as you get to the top of the ladder, use your take-down on the guard. If you knock him out, you'll find a pocket secretary on him with codes to the laser grid. You ultimate goal is to get into the room behind the level 3 security door, but with no upgrades or Praxis points, you can't hack it. You can find the code on a pocket secretary in the vents under the floor. One way to get down there is to disable the lasers, then go through the next door while avoiding the camera. The other entrances to the vent are in the northern rooms. When you have the code, you can continue exploring or go back to the locked door to get your gear. A good way to get around down the corridors with guards in them (and earn some traveler experience), is to use a crate to get up through the vent covers at the top of the wall outside, then cross the pipes above the guards. Your laser grid code will also work on the one at the other end of the passages. In the northeast room you'll find some grenades and mine templates, and in the northwest room is a security terminal, but it only controls the one camera back by the locked room, which is easy to avoid. The guard in that room has the code to the computer on a pocket secretary.
When you're done looking around, go through the door into CMPT-01 D-01 and at the end of the hall you'll find your body armor. After suiting up you'll get a mysterious call on your InfoLink.
Locate the CIC[edit]
The message is garbled, but the voice tells you to find the CIC. If you're not after the Factory Zero achievement/trophy, don't forget to grab the Praxis kits and weapon from the crates before heading out. Outside and around the corner, you'll find that the southwest door is now open and leads down a hall to an office. When you get there, you'll feel an explosion and a computer voice will inform you that one of the stasis pods' life support systems needs to be manually re-initiated. At this point you can do the Acceptable Losses side quest at the bottom of the containers, where you'll also find a reload speed upgrade.
When you go out the office window, climb up the ladder on the crates, then jump to the gantry hanging from the ceiling. The control marked "HRZTL" will move you back and forth in the direction of the side you're on, while the "VRTCL" control will move you up and down. Take the gantry back away from the objective and down a level and you can jump into one of the open crates for a 200 point experience bonus and an ammo capacity upgrade. Back on the gantry, take it back up then all the way across to the other side where you can go over the railing and down a ladder. The passages are blocked so you can only go one way, which is around to an open spot in the wall that goes out onto some more cargo containers.
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If you upgraded your legs, you can use your jump to get up on top of the containers in the southwest corner to find the spot where you were found stowed away. Down the bottom of this pile is an entrance to another passageway, which, after moving some crates, leads around to a spot where you climb up into an open cargo container. Remove the crate and crawl into the space behind it for a 300 point pathfinder bonus and some grenades. Back at the other pile of containers, head up to the northwest corner to find a ladder that will take you to the top and an open container at the bottom of it you can reach with the upgraded jump. At the top of the ladder is a hatch that leads you out onto the deck of the ship. Out of the walkway you find yourself in, there are a couple mine templates to the left and a guard you can take down to the right. The path along the west side of the building is blocked and on the other side of the blockage is a little fenced in area with a rate-of-fire upgrade inside. You can hack the level 2 security door, or just jump over the fence with upgraded legs.
If you keep heading east along the north walkway past the guard instead of taking the detour to the fenced in area, you'll see a sign that directs you up the stairs to the CIC. If you take the stairs, beware of the guard patrolling by the locked door with the camera on it. If you're feeling adventurous, you can take the catwalk cart around the west side of the building for 100 points which allows for an easier take down from the south. If you do take him out, you'll find the code to the door on a pocket secretary he carries. The good thing about going this way, is the lasers are on the fritz on this side, so you can go under them without having to hack the console.
Alternatively, you can go past the stairs and take out the guys around the corner when they finish talking and go in the unlocked door next to them. In the hallway, wait outside the door of the room where the two guys are talking on the left side. When the one on patrol comes out, if you're trying to be stealthy, take them out one at a time, being sure to move the one in the hallway out of the camera's line of sight. In their quarters you'll find a pocket secretary with a code on it and a 200 point eBook. Down around the hall past the camera is the door for the code you just found. Inside you'll find a damage upgrade and a pocket secretary with the code to the laser grid, making the bottom route a bit more lucrative for the added effort. Eventually you'll need to go upstairs to the CIC room, which is blocked off by security lasers on each side. From the upper entrance, you can also move the large crate if you upgraded your strength, which reveals a vent that goes into the CIC as well. However you do it, head inside and go into the booth behind the glass to finish the objective.
Locate the sally port[edit]
After receiving another message from the mystery caller, two guards will enter the CIC and start up patrols after a brief conversation. With upgraded hacking to level 2, you can get into the security terminal and turn off a couple cameras that will one your way out before leaving the CIC. If you want to get out unnoticed, hop the counter and use the vent there to get over by the exit. When they both have their backs turned, just head out the door. Take the stairs or the ladder down, where you'll find a door with two guys in a hallway beyond it. If you want to sneak, use the vent above the pipes and drop down between the two after they finish talking and walk away from each other. Head through the door in the middle of the passage and flank the guard that's leaning against a stack of pipes. There's a security level 2 door in the hallway with a shotgun and an ammo crate containing some grenades and a mine template in the room beyond. Follow the hall around and you'll come to an office with a computer and a security terminal, where you can turn off three of the cameras in the coming sections.
Take the passage out of the office and around the corner where you'll run into a guard with his back to you, ripe for a silent take-down. The ladderwell by him is secured with lasers, but they're intermittent, so you can drop through if your timing is good. Otherwise, continue down the hall through the next door, and you'll find a guard down the hall to your right who has the laser code on him. If you keep going down that hall with the guard in it, you'll come to an open cargo container on the side, and inside you can use the punch through walls upgrade to bust into the next container and the one after that. Or, if you have the strength upgrade, there is a moveable large crate farther into the hall and beyond it is an empty ladderwell you can fall down with the Icarus Landing System, or a real ladder that leads down to a passage with two guards. If you go all the way to the end of the passage that starts with the laser grid ladderwell, you can go up a level and turn off the gas to the passageway down where the two guards and the camera are. The gas passage and the laser ladderwell both lead to an elevator you can take down, or you can take the ladder down from the passage with the two guards in it. Either way, you find yourself in a cold storage stasis pod bay.
At the east end of the bay is a door protected by lasers that you need to get through. If you came down the elevator, you're in the northwest corner, if you went through the crates you're in the middle of the west side and if you came down the ladder, you're in the southwest corner. It's a level 3 security panel to disable the lasers, or you can find a pocket secretary in the northwest corner by the elevator. Even if you didn't come down through the cargo containers, if you have your legs upgraded you can get 300 experience points and a Praxis kit by jumping into an open container in the stack. When you've disabled the lasers in the stasis pod bay, head through the door when the guard and the camera aren't looking, then either hack the level three door in the next room for a heavy rifle, or go through the other door to a biometric security scan. Activate the scan with the button on the left, then step inside. Although the system doesn't recognize you, your hacker friend will get you through.
Locate the rendezvous point[edit]
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Head out the door to the cargo ramp where there is a machine pistol and some ammo waiting in a cargo container if you want. When you're ready to cross over, throw the switch near where you entered to lower the ramp. If you've not been stealthy, there will be some guards on the deck waiting for you, so get into the cargo container while the ramp lowers and wait for them to start patrolling. If you didn't raise any alarms however, there will be no one there and it should be a breeze to get in. Get past the guards if they're there, and head into the receiving bay. If you have set off alarms, the boxguard inside will be patrolling, and even if it isn't, it's easier take the high ground. Outside the bay, you'll find two crates you can use to get up to a ladder that will take you to a vent and an ammo capacity upgrade. This in turn leads to the beams going over the whole bay. Alternatively, you can sneak around through the bay and grab some items and experience by exploring the crates, including a reload speed upgrade in an open cargo container at the top of the stack in the northwest corner. If you're going through the ground approach, you'll need to get through the laser-guarded door in the north end, or use the vent in the northwest corner. If you took the beams above, you can cross to the other side where another vent will lead you into the next bay.
Here there are no bots, but there are plenty of guards down on the ground level and a couple turret covering the southeast sector. If you're on the ground, you can go the easier route to the north by jumping over the large crates with leg augs or by moving them with strength augmentation. If not, it's a bit longer but you can sneak through the open container by the door and along the south side, where you'll find a vent behind the stairs up to the office. In the northeast corner of this loading bay is the entrance to the maintenance tunnel. If you came through the vents above, climb out to the platform out above the main floor for an ammo crate and a Praxis kit. From there you can go back and drop down onto the office in the southwest and then either enter the office through the hole in the ceiling or climb down the ladder and go around the south wall. Be advised though, that there are two guards in the office, so unless you're looking for a fight, it's easier to skip it. You can also find a laser targeting upgrade in the blue container hanging from the gantry. When you get to the maintenance tunnel, follow it down and into a little stowaway room where you'll meet Keitner again.
Note: it will be a pay off if you're thorough when clearing the areas of enemies and searching for the hidden goodies before talking to Keitner. Also Quinn won't be available as the "Gone Fishing" sign is there until you talk to her. You also cannot get into more areas that have a large prison without her help.