The following guide will explain how to obtain Clock.exe (and the "TRUE ULTIMATE POWER" achievement) with the least effort possible.
However, if you're a new player or don't like getting things spoiled I'd advise against reading further.
This game is full of hidden paths to follow and rewards those who dare to look for more, and you'd do yourself a disservice by just spoiling yourself the fun.
If you still want to enjoy the game but don't know where to start looking, here are two different trails you can follow to reach Clock.exe:

1) (HARDER)
During a mission for CSEC you'll have to decrypt a file called C_EXE_contact.dec. Instead of just completing the mission, try reading it and going on from there.

2) (EASIER)
If you still haven't hacked jmail.com's server (seriously? That's the first thing I'd do!), do it now, and snoop around the mailboxes. One email in particular has a... clock themed subject. Go on from there.

In addition to the tools you have at your disposal right off the bat, you'll need Decypher.exe and to be able to crack at least 4 of the following services of your choosing:

HTTP WebServer (Port 80)
SSH (Port 22)
FTP Server (Port 21)
SMTP MailServer (Port 25)
SQL Server (Port 1433)
Blizzard Updater (Port 3724)

1) Pop some shells around, you'll need them to overload the proxy.
2) Connect to 24.43.69.78
3) Analyze and solve the firewall, overload the proxy and hack 4 ports. The tracing process is pretty fast so you may want to take it easy and do this point in two steps.
4) Copy the file VAULT/Clock.dec into your machine.
5) Connect to your machine and decrypt it with "Decypher Clock.dec yuna"
6) Copy Clock.exe into the binaries folder with "mv Clock.exe /bin"
7) Execute "Clock"
8) Enjoy your achievement and your new game breaking tool.