use strict;
use warnings;
use List::Util qw(first);

my @array_to_search = (1..5) x 2;
my $target_value = 3;
my @target_values = (5, 4);

{   # Find the first target and do something to it.
    my $match = first { 
        $target_value == $_ 
    } @array_to_search;
    matches_found( $match );
}

{   # Find all matches and do stuff.
    my @matches = grep { 
        $target_value == $_ 
    } @array_to_search;
    matches_found( @matches );
}

{   # match list with nested loop matching  
    my @matches;
    foreach my $target ( @target_values ) {
        push @matches, grep { 
            $target_value == $_
        }    @array_to_search;
     }
     matches_found( @matches );
}

{   # match list with a hash lookup  
    my %target;
    @target{ @target_values } = ();
    my @matches = grep {
        exists $target{$_}
    } @array_to_search; 
    matches_found( @matches );
}


##</code><code>##

if ($event eq 'JOIN') {  # indent your code.  It doesn't matter if you use tabs, 2 spaces, or 4 spaces per level, with GNU or K&R or any other bracketing.  Just pick a style and use it.

open (PROTECTED, "$protected");  
# two element open.  Global file handle in use.  No error checking.  Unnecessary stringification.

@protected = <PROTECTED>;  # You are leaving line endings on your list items.  Is this what you meant to do?  This probably why what you have now isn't working.

close(PROTECTED);  # no error checking.

for $_ (@protected) {  #WTF?  No need to add $_ to for declaration.

if ($_ eq $user[0]) {

#  Do you really need to override prototypes on your function called sock? &subroutine() has a specific meaning.  See perlsub for more info.  sock() is not very descriptive as function names go.  Try something like send_message() or send_message_to_client().
&sock("PRIVMSG $tag

:$user[0] Is A Protected User! $_");
# If you want to have multiline variables, use a heredoc.  Otherwise construct them.  Dangling lines like this is asking for trouble.  
}

}

}

##</code><code>##

if ($event eq 'JOIN') {

    # Read in protected user ids
    open (my $protected_fh, '<', $protected)
        or die "Unable to open $protected: $!\n";

    my @protected = <$protected>;
    chomp @protected;

    close(PROTECTED)
        or die "Unable to close $protected: $!\n"

    # Verify that $user[0] is not protected.
    foreach my $protected_uid (@protected) {

        if( $protected_uid eq $user[0] ) {
            sock( join "\n",
                "PRIVMSG $tag",
                '',
                ":$user[0] Is A Protected User! $protected_uid",
            );
            last;  # stop processing after first match found.
        }    
    }
}