Tools needed:

SonicGMI (Sonic Generations Mod Installer) Latest builld 1.1 RC5

NIGHTS Generations mod (You can install both but only activate one!):
Nights Fly <—  recommended!
Nights Runs

1) Installing
Unzip SonicGMI and copy the contents of the folder into the folder where SonicGenerations.exe is stored. For example: C:\Program Files(x86)\Steam\steamapps\common\sonic generations\

You should now have 4 new files and a “mods” folder in your sonic generation game folder.

Now unzip the Nights mod you chose.
We will use the Nights Fly mod for example.
Inside unzipped Nights(with fly) is folder “NIGHTS”.
Copy that folder to the inside “mods” folder in your sonic generations game folder.
Would look like this example:
C:\Program Files(x86)\Steam\steamapps\common\sonic generations\mods\NIGHTS

Now start SonicGMI.

First enable mods by clicking the install/uninstall button and it should say mods enabled.

Next click the checkbox of the mod you want in the mods window and hit the save button.

Close with the close button and start the game.