He broke into his flat, kidnapped him, drove him away to a remote spot, beat him up a bit, and dangled him upside-down with a bit of rope. Then, he threatened that he would kill him if he ever came back to Walford again.
The reason for doing it is that Sean blamed Al for shooting Sean in revenge for Sean stealing Al's girlfriend (If I remember correctly). Sean told Al that he was originally intending to kill him, and that doing 15 years in prison would be worth it. But he changed the plan at the last minute because he had unexpectedly discovered Stacey and re-connected with his family.