VR Mission 2.1
Not long into the mission, you'll meet your first Mastiff. After that, you'll come to a hallway with two more Mastiffs patrolling. You can kill both of them with stealth. With them out of the way, check your map and you'll see a small access corridor that is connected to this hallway on both ends. This VR mission is in that area on the floor.
Humanoid Dwarf Gekko 1
You'll drop down a large sewer pipe into a lower level. In the sewer that you are in, you'll find piles of rubble scattered around and Dwarf Gekkos hanging from the ceiling. Kill them all and then return to where you initially dropped down to find your first Humanoid Dwarf Gekko.
VR Mission 2.2
Later on in the mission, you'll fight your first Raptor. When you finish that fight, go up ahead and through the door on the left. You should enter a room with some machinery in it and you'll also find your first [Cardboard Box] in this room. The VR mission is just to the left of the door you entered through.
Data 2.1
You'll enter a long sewer section with three Mastiffs just after acquiring your first cardboard box. About 3/4 of the way down, you'll see some white pipes coming up out of the ground on the left side. On top of these pipes will be a [Blade Box] with this data in it.
Man in Box 2
After getting your first cardboard box, you'll sneak through a long hallway with three Mastiffs in it. When you get through this room, you'll find yourself on a small lip above a lower ring shaped tunnel. This is the room in which you find the secret entrance to the research facility. You'll see a small room in the middle of the ring. Cut through the gate to get into it and you'll find Man in Box 2 here.
Left Hand 2.1
There will be a cutscene involving a room filled with cybernetic brains and when it ends, you'll find yourself in the room you were previously in. You'll initially be attacked by three guards but a fourth will show up shortly by coming out of a side door. This fourth guard has this left hand.
Data 2.2
You'll take control of a Dwarf Gekko for part of the mission and when you do, you'll find yourself in a U-shaped room. On the right wall of this room, you'll find a small vent that the Gekko can slide into by performing a Ninja Run and hitting Heavy Attack. The Data is in this vent.
Data 2.3
In this same U-shaped room, follow the bottom floor of this room forward and then turn left. At the second turn in the U stop and look for the stack of crates in the corner to the right. The Data is on this stack of crates.
Left Hand 2.2
After the section where you control the Dwarf Gekko, run into the same room with Raiden and one of the guards on the bottom floor will have this arm. Remember that if you stunned enemies with the Dwarf Gekko, he may be lying on the floor unconscious.
Life+ 2
You'll reach a point where you have to use a Dwarf Gekko to open a door and after you are done with the Gekko, you'll enter the same area as Raiden. Climb up to the catwalks on the upper level. If you follow them to the end (it should lead back towards the entrance of the room), you should find a [Blade Box] with this item inside.
Left Hand 2.3
After the section with the Dwarf Gekko, you'll enter the same room with Raiden. Open the door on the bottom floor to continue and you'll enter a hallway. You'll eventually come to a pair of guards in a hallway. One of them will have this hand.
VR Mission 2.3
Just before finishing the mission, you'll enter a room where they are preparing a freezing process for human organs. When you finish your chat, immediately turn right and you'll find the VR mission in the corner of this room.
