i really hate your style =/ soooooo i decided to edit your code in my style. look over it.

on *:TEXT:*:#: {
  tokenize 32 $strip($1-)
  var %w = !countdown,!viewcount,!countstarted,!countstop,!countpause,!countrestart
  if ( %flood $+ $nick == $null ) {
    set -u2 %flood $+ $nick 1
    if ($1 == $gettok(%w,1,44)) {
      if (%count) { msg $chan There is a game going already | halt }
      if ($2 >= 100001) { msg $chan Sorry number is to big | halt }
      if (!$2) { msg $chan Usage: !countdown (second) | halt }
      set -z %count $2 | msg $chan It will now count down from $2, to view it type !viewcount | set %count2 $2 | set %count3 $nick 
    }
    if (!%count) {
      if ($1 == $gettok(%w,1,44)) {
        if ($v1 = 1) { msg $chan Countdown is now over from %count2 | unset %count2 | unset %count3 | halt }
        msg $chan %count | var %t $calc(%count2 - %count) | var %t2 $duration(%t) | msg $chan I have been running for %t2 
      }
      if ($1 == $gettok(%w,1,44)) {
        msg $chan The count was set to %count2 and $calc(%count2 - %count) seconds has gone by so far, the count was started by %count3 | var %t $calc(%count2 - %count) | var %t2 $duration(%t) | msg $chan Count can be stopped by %count3 with !stopcount, i have been running for %t2 
      }
      if ($1 == $gettok(%w,1,44)) {
        if ($nick !== %count3) { msg $chan You didn't start the count  | halt }
        msg $chan Count stopped by $nick it was set to %count2 and $calc(%count2 - %count) seconds had passed | unset %count %count2 %count3 %countpause
      }
      if ($1 == $gettok(%w,1,44)) {
        if ($nick !== %count3) { msg $chan You didn't start the count | halt }
        set %countpause %count | msg $chan Count is now paused, to start is again tpye !countrestart | unset %count
      }
      if ($1 == $gettok(%w,1,44)) {
        if (%countpause) {
          if ($nick !== %count3) { msg $chan You didn't pause or start the count | halt }
          msg $chan Count started after stop | set -z %count %countpause
          halt
        }
        msg $chan The count was never paused
      }
    }
    msg $chan No countdown started 
  }
}