Ok i hope this is not a silly queston i wan't to know how can i change the lua that the republic is fighting againts the imperials

C:/Program Files/LucasArts/Battlefront2/gamedata/data/_LVL_PC/Mission.lvl

First choose the level you want to change the sides for (ex. Kam1cw) next type in the level name in the search or find bar in the hex editor program. If you don't have one I suggest hex Workshop. Once you type in the name of the level you want to mod (ex. kam1cw (kamino clone wars)) you will see the republic and CIS sides. Change all the CIS troopers into IMP troopers by replacing the letters "CIS" with "IMP".
Replace:
SIDE\cis.lvl......cis_inf_rifleman......cis_inf_rocketeer......cis_inf_engineer......cis_inf_sniper......cis_inf_droideka......CIS_inf_officer......cis_hero_jangofett......
with:

SIDE\imp.lvl......imp_inf_rifleman......imp_inf_rocketeer......imp_inf_engineer......imp_inf_sniper......imp_inf_droideka......imp_inf_officer......imp_hero_jangofett......

Both names highlighted in red will not appear in the level unfortunetly... Someone else could probably explain this better.

You could do what Jango_Fett_A is suggesting, but that will affect every map in your game. If you are making your own map with the modtools, you will want to do some lua editing. Read the Jedi Creation Doc included with the modtools to learn how to modify units.

Take whichever lua you're using, and replace the lines referring to the side you want out with lines that refer to the side you want in. It's just a matter of copying and pasting information from one lua to another. The sound lines (for the faction announcer) I can't guarantee will work across eras, because I'm not familiar with how exactly sound is done in the game, but changing the units out should be easy enough. All that is required is that you have the side files set up as well.

ok thank you all for your help because in the 3rd map of the 22D story the place will take on kamino where the galactic federation made their own army of clones the armor 4 clones not stormtrooper's

Sounds something like the campaign mode on Kamino where they have the imps fighting the clones.

yup it sound's like that but the republic will fight against the armor 4 clones