Fallout3.esmAnchorage.esmThePitt.esmBrokenSteel.esmPointLookout.esmZeta.esmCRAFT.esmCALIBR.esmProject Beauty.esmVault 101 Revisited.esmCubeExperimental (EN).esmMothership Crew.esmEVE.esmFOOK2 - Main.ESMFOOK2 - [DIK] DLC Improvement Kit.ESMFO3 Wanderers Edition - Main File.esmMart's Mutant Mod.esmRTS NW.esmRH_IRONSIGHTS.esmFO3 Wanderers Edition - Alternate Travel.espDarNifiedUIF3.espProject Beauty- Broken Steel.espProject Beauty- Point Lookout.espCASM.espRH_IronSights_Basic_VanillaPlugin.espRH_IronSights_Basic_AnchoragePlugin.espRH_IronSights_Basic_PittPlugin.espRH_IronSights_Basic_BrokenSteelPlugin.espRH_IronSights_Basic_PointLookoutPlugin.espRH_IronSights_Basic_ZetaPlugin.espRH_IronSights_Pitt_NewRifleSights.espRH_IronSights_RemoveReticule.espRH_IronSights_PL_NewItems.espGalaxyNewsRadio100[M].espAQFH.espAQFH2.espHeirApparent.espNotSoFast.espMTC Wasteland Travellers.espMTC Wasteland Travellers (Optional)- Crowded Cities.espMegaton House and Theme Overhaul.espFOOK2 - Main.espFOOK2 - Project Beauty.espFOOK2 - [DIK] DLC Improvement Kit.espFOOK2 - Main [Hotfix].espFOOK2 - DIK [Hotfix].espFO3 Wanderers Edition - Main File.espFO3 Wanderers Edition - DLC Anchorage.espFO3 Wanderers Edition - DLC The Pitt.espFO3 Wanderers Edition - DLC Broken Steel.espFO3 Wanderers Edition - DLC Point Lookout.espFO3 Wanderers Edition - DLC Mothership Zeta.espFO3 Wanderers Edition - Followers Enhanced (BrokenSteel).espFO3 Wanderers Edition - Optional Restore Tracers.espFO3 Wanderers Edition - Optional VATS Halftime.espFO3 Wanderers Edition - Optional Restore Tracers (automatics only).espFO3 Wanderers Edition - Project Beauty.espFO3 Wanderers Edition - Project Beauty (Followers Enhanced).espRH_FWE_Bridge.espWeaponModKits.espWeaponModKits - FWE Master Release.espWeaponModKits - OperationAnchorage.espWeaponModKits - ThePitt.espWeaponModKits - BrokenSteel.espWeaponModKits - PointLookout.espWeaponModKits - Zeta.espWMK-RH IronSights.espEVE.espEVE Operation Anchorage.espEVE - FWE Master Release.espEVE - FWE Master Release (Follower Enhanced).espEVE Anchorage - FWE DLC Anchorage.espEVE - FWE with WeaponModKits.espRH_EVE_Bridge.espMart's Mutant Mod.espMart's Mutant Mod - DLC Anchorage.espMart's Mutant Mod - DLC The Pitt.espMart's Mutant Mod - DLC Broken Steel.espMart's Mutant Mod - DLC Point Lookout.espMart's Mutant Mod - DLC Zeta.espMart's Mutant Mod - Zones Respawn.espMart's Mutant Mod - Tougher Traders.espMart's Mutant Mod - Natural Selection.espMart's Mutant Mod - Master Menu Module.espMart's Mutant Mod - Project Beauty.espMart's Mutant Mod - Project Beauty + FWE.espMart's Mutant Mod - FOOK2.espMart's Mutant Mod - FOOK2 - DIK.espMart's Mutant Mod - FWE Master Release.espMart's Mutant Mod - FWE Master Release + DLCs.espMart's Mutant Mod - FWE Master Release + Project Beauty.espFasterMorePowerfulMines.espFOOK2 - RH_IronSights.espAQFH_D_103.espFOOK - DIK - Project Beauty.espMerged.espTotal active plugins: 96Total plugins: 96

I am having an issue with the follower script. It states when I start the game that something modified the script and it probably won't work correctly.

Go easy, while I have good experience working with mods in Oblivion, I have never really touched fallout before. I have probably made some stupid mistakes. Thanks for any help that you can see.

I did run BOSS and FO3Edit

FOOK2 and FWE are incompatible. They're both overhauls changing many of the same things. Pick one of them to play with and remove all of the plugins and patches associated with the other one. The message you're getting is most likely being thrown up because of that conflict.