It's works fine. Just one suggestion: Remove the !finished command and make it declare the results automatically, as soon as both the players have chosen.

try this:

on *:text:!RPS:$chan: {
  if ( %RPS == $null ) {
    msg # 4 $+ $nick 14has started 9ROCK, PAPER, SCISSORS! 
    msg # 14 $+ Who would like to accept 4 $+ $nick $+ 's 14challenge? Just type 8!Accept
  set %RPS 1 | set %challenger1 $nick | Halt }
  if ( RPS != $null ) { msg # 14There is currently a game of RPS going on. }
}
on *:text:!Accept:$chan: {
  if ( %RPS == 1 ) { msg # 9 $+ $nick 14has accepted 4 $+ %challenger1 $+ 's 14challenge. | set %challenger2 $nick | set %RPS 2 | msg # 14To Chose Rock, Paper, or Scissors, Type 8/Notice $me <Rock, Paper, Scissors> }
  if ( %RPS == $null ) { msg # 14You must first initiate the RPS game by saying 8 $+ !RPS }
}

on *:text:!End:$chan: {
  if ( $nick == %challenger1 || $nick == %challenger2 || $nick isop #Ethan ) {
    msg # 4 $+ $nick 14has decided to call it quits. | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt
  }
  if (( $nick != %challenger1 ) && ( $nick != %challenger1 ) && ( $nick !isop #ethan )) { 
    msg # 14 $+ You must be participating to end the RPS duel. 
  }
}

on *:notice:*:?: {
  if ( %RPS == 1 ) { notice $nick There has to be 2 contenders. }
  if ( %RPS == 2 ) { 
    if ( $nick == %challenger1 ) {
      if ( $1 == Rock ) { notice %challenger1 You've chosen Rock. | set %challenger1.choice 1 }
      if ( $1 == Paper ) { notice %challenger1 You've chosen Paper. | set %challenger1.choice 2 }
      if ( $1 == Scissors ) { notice %challenger1 You've chosen Scissors. | set %challenger1.choice 3 }
      if (( $1 == $null ) || (( $1 != Rock ) && ( $1 != Paper ) && ( $1 != Scissors )) { notice %challenger1 You must choose Rock or Paper or Scissors }
    }
    if ( $nick == %challenger2 ) {
      if ( $1 == Rock ) { notice %challenger2 You've chosen Rock. | set %challenger2.choice 1 }
      if ( $1 == Paper ) { notice %challenger2 You've chosen Paper. | set %challenger2.choice 2 }
      if ( $1 == Scissors ) { notice %challenger2 You've chosen Scissors. | set %challenger2.choice 3 }
      if (( $1 == $null ) || (( $1 != Rock ) && ( $1 != Paper ) && ( $1 != Scissors )) { notice %challenger2 You must choose Rock or Paper or Scissors }
    }
    if (( $nick != %challenger1 ) || ( $nick != %challenger2 )) { notice $nick You'll have to wait until a free round if you want to play. }
  }
  if ( %RPS == $null ) { /notice $nick You must first initiate the game by saying !RPS and then follow the instructions. }
}

on *:Text:!Finished:#chan: {
  if ( %RPS == $null ) { msg # 14You must first initiate RPS by typing !RPS }
  if ( %RPS == 1 ) { msg # 14You need 2 contenders before the game can start. }
  if ( %RPS == 2 ) { 
    if ( $nick != %challenger1 && $nick != %challenger2 ) { msg # You must be a contender in order to finish the round. | Halt }
    if ( %challenger1.choice == $null || %challenger2.choice == $null ) { msg # 14You must wait for 11both 14contenders to decide on their weapon. }
    if ( %challenger1.choice != $null && %challenger2.choice != $null ) {
      if ( %challenger1.choice == 1 && %challenger2.choice == 1 ) { msg # 4 $+ %challenger1 14chose: 8Rock. 9 $+ %challenger2 14chose: 8Rock. 4TIE GAME! NO WINNER! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
      if ( %challenger1.choice == 1 && %challenger2.choice == 2 ) { msg # 4 $+ %challenger1 14chose: 8Rock.  9 $+ %challenger2 14chose: 8Paper. 9 $+ %challenger2 14has beaten 4 $+ %challenger1 $+ 14!!! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
      if ( %challenger1.choice == 1 && %challenger2.choice == 3 ) { msg # 4 $+ %challenger1 14chose: 8Rock. 9 $+ %challenger2 14chose: 8Scissors.  4 $+ %challenger1 14has beaten 9 $+ %challenger2 $+ 14!!! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
      if ( %challenger1.choice == 2 && %challenger2.choice == 1 ) { msg # 4 $+ %challenger1 14chose: 8Paper. 9 $+ %challenger2 14chose: 8Rock. 4 $+ %challenger1 14has beaten 9 $+ %challenger2 $+ 14!!! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
      if ( %challenger1.choice == 2 && %challenger2.choice == 2 ) { msg # 4 $+ %challenger1 14chose: 8Paper. 9 $+ %challenger2 14chose: 8Paper. 4TIE GAME! NO WINNER! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
      if ( %challenger1.choice == 2 && %challenger2.choice == 3 ) { msg # 4 $+ %challenger1 14chose: 8Paper. 9 $+ %challenger2 14chose: 8Scissors. 9 $+ %challenger2 14has beaten 4 $+ %challenger1 $+ 14!!! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
      if ( %challenger1.choice == 3 && %challenger2.choice == 1 ) { msg # 4 $+ %challenger1 14chose: 8Scissors. 9 $+ %challenger2 14chose: 8Rock.  9 $+ %challenger2 14has beaten 4 $+ %challenger1 $+ 14!!! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
      if ( %challenger1.choice == 3 && %challenger2.choice == 2 ) { msg # 4 $+ %challenger1 14chose: 8Scissors. 9 $+ %challenger2 14chose: 8Paper. 4 $+ %challenger1 14has beaten 9 $+ %challenger2 $+ 14!!! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
      if ( %challenger1.choice == 3 && %challenger2.choice == 3 ) { msg # 4 $+ %challenger1 14chose: 8Scissors. 9 $+ %challenger2 14chose: 8Scissors. 4TIE GAME! NO WINNER! | unset %challenger1 | unset %challenger2 | unset %RPS | unset %challenger1.choice | unset %challenger2.choice | halt }
    }
  }

choose between paper, scissors and stone, and bet your points

you choose paper and betting 50 points, waiting for my turn

1 minute later .....

I choose rock, rock beats paper and you lose 50 points
this is what i'm talking about, and nobody makes this game

There are a couple of things I would've done differently, like there's no real reason to halt the script if %RPS is false (!%RPS or %RPS == $null) and instead of checking if $1 is null or != rock I'd use if/else if/else if/else.

Looks nice could be a bit shorter. Something you could do is "if ( %RPS == $null )" to "if (!%RPS)" it's the same thing but less typing, for your on notice add a else so if they type papr or rokc as a typo it well notice them back that there was an error and show to commands or words they can use.

idk many of the $command things. :/ although i could have 3 statements for the first player, then the diff outcomes of %challenger2.choice. :L

lol my bad, but yeah thatta way it will work on all channels.

lol. i was ganna say... :L never saw that one :P

Too many if statements, it all looks the same.

Also, I'm sure there's a better way to decide who won rather than those 9 if statements.

One more thing, add halt's for things you don't want, like the !rps !accept thing I told you about.

ooo. its not %chan its $chan dollar sign

no $chan is all chans... change it!

%chan? but wouldnt you have to set it? or is it a preset var with the current chan? o.O

rating: 5 (average)
reason: change #ethan to $chan. code is mediocre meaning sloppy.

You should change #ethan to %chan or #