Mass Effect as in the first game has a blitch that seems to happen with AMD users. The black boxes appears on Shepard and the two squad members in both Peak 15 and Ilos. A temporary fix involves to use the console and typing in a command which lightens up the the game giving view once again but it is recommend to switch it off after completely both sections.
If your not savvy with Computers and Coding I suggest you don’t do this. If you do its o your own risk! I’m sharing this for my own personal use.
1) Inside your ~/Documents/BioWare/Mass Effect folder open BIOInput in a text editor.
2) Add line ConsoleKey=Tilde under [Engine.Console]. This enables the console.
3) In game, when the glitch crops up, hit the Tilde key (~) to open the console and type viewmode unlit. Press Enter and close the console.
This is only a temporary fix. The lighting will look a bit strange while it is active.
4) Type viewmode lit in console to disable. Or restart the game.
The console has a handy History function. Use the arrow keys to access previous console commands.