my $tools = new TOOLS;

$tools->SUPER::Callme(); # it should call the AGENT::Callme
$tools->Callme();
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If you need to do this outside of the TOOLS package, you're doing something very wrong. The code that's using the $tools object should not need to know or care what $tool's inheritance chain is. If your TOOL's Callme() cannot work without also using AGENT::Callme(), then you should set it up so that AGENT::Callme is called automatically from TOOL::Callme, not rely on the user to do it for you. Same goes for new().

package TOOLS;

sub new {
  my ($package) = @_;
  my $self = $package->SUPER::new();
  # do other stuff, or remove this whole sub if
  # you're not acutally doing anything in this 
  # method and let AGENT's new() method do all the work.
  return $self;
}

sub Callme {
  my ($self) = @_;
  $self->SUPER::Callme();
  # do stuff.
}
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As explained by someone else above, you can't (and shouldn't) use SUPER outside of the package that is the subclass.