The eye of the category two storm has now moved past the city but emergency services say it's still not safe to go outside.
Marcus is now headed towards the Timor Sea and is expected to hit Western Australia's Kimberley Coast on Sunday, bringing wind gusts of up to 150km/h.
The storm brought down hundreds of powerlines and trees and damaged property across Darwin and also affected the city's drinking supply.
Residents have been told to boil drinking water as a precaution until further notice.
Meanwhile, water police were called out to rescue two people from two boats that collided after one of them slipped its moorings in Sangove Creek as the storm struck.

The eye of the category two storm has now moved past the city but emergency services say it's still not safe to go outside
Residents have been told to stay inside and emergency services are only responsible for critical incidents until the category two storm passes.
However, some residents did not mind the cyclone and decided to enjoy a beer in a swimming pool for a friend's birthday.
A warning zone is currently in place from Cape Hotham to Mitchell Plateau, including Darwin and southern parts of the Tiwi Islands.
Flights in and out of Darwin have been cancelled and businesses have been told to close their doors, though some had opened early on Saturday to let customers purchase supplies.
Northern Territory locals shared the trail of destruction left by Tropical Cyclone Marcus which include roofs being ripped off and sheds being blown upside down.
Walking paths and roads have become unusable with huge tree trunks and branches littering the thru ways with one local saying they hadn't seen a street without a tree down.
Street signs were torn from the ground while an iconic McDonald's sign was also destroyed.
Marcus' presence was felt with entire root systems of decade old trees were pulled out of round-a-bout centres and fans were left bent.

Residents have been told to stay inside and emergency services are only responsible for critical incidents until the category two storm passes
Despite warnings to remain inside, one local reported seeing a line of cars stretching down the street from a bottle shop ten minutes after it re-opened.