Try changing:

Code:
  if (!$isfile($+(Naruto RPG\,$nick,.stats,.txt))) {


to:

Code:
  if ($isfile($+(Naruto RPG\,$nick,.stats,.txt))) {


So you're left with..

Code:
on *:Text:!Chr *:?: {
  if ($isfile($+(Naruto RPG\,$nick,.stats,.txt))) {
    var %do.cmd = write $+("Naruto RPG\,$nick,.stats,.txt")
    if ($2 == Sasuke) {
      write -c $+("Naruto RPG\,$nick,.stats,.txt")
      %do.cmd Character: $2
      %do.cmd Level: 1
      %do.cmd Attack: 6
      %do.cmd Defence: 4
      %do.cmd Speed: 6
      msg $nick You have chosen $2 as your character.
      msg $nick To view Sasuke's attacks type !Attacks
    }
    if ($2 == Sakura) {
      write -c $+("Naruto RPG\,$nick,.stats,.txt")     
      %do.cmd Character: $2
      %do.cmd Level: 1
      %do.cmd Attack: 6
      %do.cmd Defence: 4
      %do.cmd Speed: 6
      msg $nick You have chosen $2 as your character.
      msg $nick To view Sakura'a attacks type !Attacks
    }
  }
  else { msg $nick You aren't registered. }
}


-Andy