Create a boot-able DVD or USB stick and do a fresh install from that. I would go with the USB stick as you can reuse it.
Via update manager.
Ubuntu 9.04 is not supported anymore so you will need to edit /etc/apt/sources.list
to do this. Full instructions here https://help.ubuntu.com/community/EOLUpgrades
Note: if you take the upgrade path you will need to update from 9.04 to 9.10 which is also unsupported so you will need to edit /etc/apt/sources.list again.
Then to 10.04 which is both supported and is an LTS release, though support runs out this April. From 10.04 you can upgrade to 12.04 the next LTS release.
You can then upgrade to 12.10 the latest release if you want.
A lot has changed between 9.04 and 12.10 so I would recommend a clean install however.
Make sure you have good backups in case things go wrong.