Best Answer Kelmych , 30 January 2016 - 01:24 AM
You should not have problems starting FO3 through FOSE using Mod Organizer. The installation process details are in the Fallout 3 guide here on the STEP site. When using Mod Organizer Steam itself is not typically used. The FalloutLauncher replacer for Steam, which is described in the guide, allows Mod Organizer to "hook" Steam while starting the game to allow Steam overlays. There have been other attempts to allow Mod Organizer to hook Steam when starting FO3 (using FOSE or the Fallout Launcher) but AlexxEGs is the only one I know of that seems fairly robust. Note that the FalloutLauncher replacer isn't required to get FO3 running with Mod Organizer, it just allows Steam to be connected to the game.
If you still have questions let us know; I suggest asking these questions in the Support thread for the Fallout 3 guide. There are cases where users have had problems getting FO3 to start when using Mod Organizer even when following the steps in the guide; we don't know why this happens.Go to the full post