If it's an Invasion server, then you can e.g. copy media/packages/vanilla/scripts/start_invasion.php to start_my_invasion.php, and edit it. You'll find
Code:
   // customize settings 
   // (you could copy start_invasion.php to start_my_invasion.php, customize it, and start it instead of the original, too,
   // would avoid losing settings customization when there's an update in this particular file)
   $s = &$metagame->user_settings;
   // e.g.
   /*
   $s->fellow_capacity_factor = 1.05;
   $s->fellow_ai_accuracy_factor = 0.94;
   $s->enemy_capacity_factor = 1.0;
   $s->enemy_ai_accuracy_factor = 0.94;
   $s->xp_factor = 0.27;
   $s->rp_factor = 1.0;
   $s->faction_choice = 0;
   $s->completion_variance_enabled = true;
   $s->friendly_fire = 0;
   $s->initial_xp = 0.0;
   $s->initial_rp = 0.0;
   $s->player_ai_compensation_factor = 1.0;
   $s->player_ai_reduction = 0;
   $s->base_capture_system = "any"; // could be single for backdoor prevention, not really that useful in invasion
   $s->overlay_paths = array();
   */
The stuff between /* */ is commented out, so they have no effect unless you move some of that stuff outside the comment block. To have Brownpants playable, you could have it say
Code:
$s = &$metagame->user_settings;
$s->faction_choice = 2;
That makes the third faction declared by media/packages/vanilla/scripts/gamemodes/invasion/map_rotator_invasion.php 	get_available_faction_configs() to become the friendly/coop/player faction, 0->green, 1->grey, 2->brown.
Then instead of running start_invasion.php, you'd run start_my_invasion.php.