The Long Way Home

The Long Way Home is the fourth and final mission in Deus Ex: Human Revolution - The Missing Link DLC.

Visit Quinn's shop to get supplies (optional)
If Adam managed to save the prisoners, Dr. Kavanagh or both, Quinn will applaud him enthusiastically and reveal that he left some supplies in his shop in the Maintenance Area before escaping Rifleman Bank Station to help against Pieter Burke in the upcoming confrontation.

Getting there can be difficult due to heavily increased security forces, bots and some corridors being covered with frag mines.

Recommended route is through the vent system.

Once in Quinn's shop you may want to move some boxes in the backroom to reveal a hidden switch. It will open a Quinn's Secret Store (achievement), with some guns and upgrades, as well as a level 5 locked computer. Hacking it will reveal that Quinn is not who he seems to be.

If you used the Trauma Kit on the Hyron drone in the Seafloor Laboratories, the top level 5 locked safe in Quinn's shop will be opened. Otherwise, it will need to be hacked to obtain the contents.

Fulfilling this objective will net 2400 XP.

Confront Burke
Burke is hiding inside a control room in Loading Bay 3. To reach it, Adam needs to traverse well-guarded Loading Bay 1 and 2.

Get into Loading Bay 2
There is a shortcut however, by hacking the door to Loading Bay 2 (Level 5) and sneaking to the left corner to the corridor leading to Loading Bay 3.

Another option is to get on the top level of Loading Bay 1 machine (there is a sniper position there), to do this you must pick up some boxes stored in the SW corner of the room. Beware of EMP mine and look for a pocket secretary with turret codes under boxes. If you throw boxes on top of the nearby container (you may need to wait for soldiers to calm down after all the noise, and from there you can throw them on top of the control room. Once all is quiet, you just have to climb the ladder, stack the boxes, and jump over to the rails. It is fairly easy to do a take down on sniper (if you are playing for Factory Zero achievement) and get a praxis kit and some ammo (if not) . From rails you can get to shaft leading to Bay 2.

Get through Loading Bay 2
The exit you nex you is SE corner of the room, if you snuck through level 5 door or a top vent shaft, it is rather easy to sneak past turret to the corridor.

You can also reprogram the turrets to do killing for you, PA with code is located in control room.

Defeat Burke and his men
Burke is guarded by a heavy and some medium guards, two snipers and a 80-X Boxguard. Burke himself is quite easy to take down, either lethally or non-lethal. For example, you can throw a single gas grenade into his control room (on the Give me a Challenge difficulty), or sneak up to him through a hole in the roof and perform a takedown.

Go to Loading Bay 2's docking platform
Adam just has to head back to the Hei Zhen Zhu's cargo ramp just outside of Loading Bay 2 to find Garvin Quinn waiting for him. You will have a short conversation with Quinn, who discloses himself to be the mysterious voice from the previous missions. He also admits to having utilized both you and Keitner for his and his anonymous employer's causes before sending Jensen to another Belltower secret facility in another stasis pod aboard another cargo ship. The ending sequence shows a freight helicopter carrying the container with Adam's stasis pod to the ship.

Get my equipment and get into the stasis pod
Note: This objective exists only in Deus Ex: Human Revolution - Director's Cut.

Right after talking to Quinn, you'll have to manually choose to enter the stasis pod. Before doing so, though, there will be a pocket secretary nearby with a message from Quinn, and an ammunition case. The ammunition case contains all inventory items you had before stowing away — ammo, grenades, energy bars, etc. — except for your weapons. (Your weapons themselves could be found back on the Hei Zhen Zhu, during the Getting out of the frying pan mission.)