The final boss. You have to shoot his head until he opens up the top of his skull. The gluon gun is useful here.
Destroy the orange crystals to prevent him from regenerating health. Hide behind the spike to avoid any damage. Once you deal enough damage to him and he opens his head use the jump pad to get above him and shoot the crystal inside his skull. A single rocket should do the trick.
When you defeat him, he will start to twitch and lasers will come out.
You will be teleported in the presence of the G-man. He was following your progress with interest.
He will offer you a job you cannot refuse.
Jump inside the portal to end the game. If you don't do it the game will end in another non-canon way.