Mission 0: Scientist door time saver After you kill the spider bots to help the scientist, stand near the computer so he can skip some of the talking, Then when he starts activating the computer, disarm him so you can skip the animation. (This next part is for perfect and dark agent as they cannot be killed) once you open the door after you get the escort the scientist objective, you can kill the scientist, so you don't have to wait for them and you can just run.

Mission 3: Flood gate skip It is the building with the stairs where you fight killian. You go down 1 building, then you should roll back when you are falling the next building, you should be out of bounds with this, It makes opening the flood gates quicker, you skip the enemies, and is faster.

Mission 5: Time saver This glitch requires an explosive (plasma gun recommended) You just shoot the controls with the explosive, and Chandra should say that the cells are now open. Then just kill the enemies and look for Jack.

Mission 11: Squad Skip For this skip, you will need a gadget other than the demo kit. The first part is if you are doing agent or secret agent. (ends at 1:07) The second part is for perfect or dark agent. It is just hitting both door switches quickly. This glitch allows you to continue the mission without the institute squad, which is great because they die fast, but the only problem is that Johnathan is stuck and unable to move due to him sitting (this is why you have to shoot him for perfect and dark agent). Which soft locks you at the final objective which requires Johnathan to activate the radar.