A 26-year-old Sunbury man has been charged with discharging a firearm at a vehicle, reckless conduct endangering serious injury and prohibited possession of a firearm.
Another Sunbury man, 18, faces the same charges and is also accused of armed robbery.
A 33-year-old homeless man is charged with discharging a firearm at a vehicle, and reckless conduct endangering serious injury.
They were remanded in custody to appear in Melbourne Magistrates Court on Wednesday.
The dog squad, specialist response units and police helicopters were also sent as back up in the early hours of Tuesday morning to find the suspects, sedan and shotgun.
Three McDonald’s employees and four police were escorted out of the restaurant.
A witness told The Age how police spent several hours negotiating with one of the men who was believed to be holed up in his mother’s home in Sunbury.
Heavily armed police “had the place surrounded”, the man said.
“I woke up to the sound of the megaphone saying ‘We’ve got the place surrounded, you’ve got to come out of the house’,” the man said.