When you reboot, what you actually do is change the runlevel to 6. In /etc/init.d you can find all kinds of scripts that are started/stopped when entering specific runlevels. This is where your script should live (or be symlinked to).
Now change into /etc/rc6.d. You see lots of symlinks to the scripts in /etc/init.d. Some start with a K, some start with an S. When changing to runlevel 6 (read: you execute a shutdown -r now), the services that start with a K will be stopped, the ones starting with an S will be started. (See where I'm going?)
The number after K or S is an indication of the order in which these scripts will be run.
Code:
root@k2:/etc/rc6.d# ls -l
total 0
lrwxrwxrwx 1 root root 18 Apr 4 2001 K10ipchains -> ../init.d/ipchains
lrwxrwxrwx 1 root root 14 Mar 26 2001 K11cron -> ../init.d/cron
lrwxrwxrwx 1 root root 17 Mar 26 2001 K12kerneld -> ../init.d/kerneld
lrwxrwxrwx 1 root root 16 Apr 4 2001 K20apache -> ../init.d/apache
lrwxrwxrwx 1 root root 15 Mar 26 2001 K20inetd -> ../init.d/inetd
lrwxrwxrwx 1 root root 17 Mar 26 2001 K20logoutd -> ../init.d/logoutd
lrwxrwxrwx 1 root root 17 Mar 26 2001 K20makedev -> ../init.d/makedev
lrwxrwxrwx 1 root root 17 Apr 4 2001 K20postfix -> ../init.d/postfix
lrwxrwxrwx 1 root root 16 Dec 9 2003 K20rinetd -> ../init.d/rinetd
lrwxrwxrwx 1 root root 15 May 9 2003 K20snmpd -> ../init.d/snmpd
lrwxrwxrwx 1 root root 13 Mar 29 2001 K20ssh -> ../init.d/ssh
lrwxrwxrwx 1 root root 19 Jan 26 2005 K20tivoli-sm -> ../init.d/tivoli-sm
lrwxrwxrwx 1 root tiggr 15 Apr 12 2001 K21resin -> ../init.d/resin
lrwxrwxrwx 1 root tiggr 13 Apr 9 2001 K23ntp -> ../init.d/ntp
lrwxrwxrwx 1 root root 20 Dec 6 2003 K25hwclock.sh -> ../init.d/hwclock.sh
lrwxrwxrwx 1 root tiggr 25 Jul 10 2002 K25nfs-user-server -> ../init.d/nfs-user-server
lrwxrwxrwx 1 root 1005 15 Oct 10 2003 K25resin -> ../init.d/resin
lrwxrwxrwx 1 root root 19 Mar 26 2001 K30setserial -> ../init.d/setserial
lrwxrwxrwx 1 root tiggr 17 May 23 2002 K50proftpd -> ../init.d/proftpd
lrwxrwxrwx 1 root tiggr 14 Apr 20 2003 K85bind -> ../init.d/bind
lrwxrwxrwx 1 root root 13 Mar 26 2001 K89atd -> ../init.d/atd
lrwxrwxrwx 1 root root 15 Apr 4 2001 K89klogd -> ../init.d/klogd
lrwxrwxrwx 1 root root 18 Mar 26 2001 K90sysklogd -> ../init.d/sysklogd
lrwxrwxrwx 1 root root 17 Mar 26 2001 S10portmap -> ../init.d/portmap
lrwxrwxrwx 1 root root 18 Mar 26 2001 S20sendsigs -> ../init.d/sendsigs
lrwxrwxrwx 1 root root 17 Mar 26 2001 S30urandom -> ../init.d/urandom
lrwxrwxrwx 1 root root 22 Mar 26 2001 S31umountnfs.sh -> ../init.d/umountnfs.sh
lrwxrwxrwx 1 root root 20 Mar 26 2001 S35networking -> ../init.d/networking
lrwxrwxrwx 1 root root 18 Mar 26 2001 S40umountfs -> ../init.d/umountfs
lrwxrwxrwx 1 root root 16 Mar 26 2001 S90reboot -> ../init.d/reboot