The Extinction Rebellion stunt saw protestors lie on the ground in the main hall under the giant blue whale skeleton at the popular museum on a busy day over the bank holiday weekend.
Last night, the group moved back to Marble Arch, the only police-sanctioned protest space, where they are said to be discussing their next move.
Organisers from the group Extinction Rebellion described the stunt as a "die in" created to demonstrate the threat to the planet.
Oxford Circus and Parliament Square were re-opened to traffic on Sunday, they said, while Waterloo Bridge was cleared overnight.
The teenager told a cheering crowd at Marble Arch on Sunday "we are the ones making a difference - we the people in Extinction Rebellion and the children's School Strike for the Climate - we are the ones making a difference".
A total of 963 arrests have been made since Monday in connection with the ongoing protests, with 42 people charged, Scotland Yard said.
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Farhana Yamin, the group's political co-ordinator, said being able to pause the protests showed it was an "organised and a long-term political force to be reckoned with".
Mr Khan said 9,000 police officers had responded to the protests, which had proved "extremely challenging for our over-stretched and under-resourced police".
XR members will commit to no further disruption in exchange for the mayor of London, Sadiq Khan to speed up the implementation of the Declaration of Climate and Ecological Emergency.
Boris Johnson, Mr Khan's predecessor as mayor, wrote in the Daily Telegraph that he was "not in favour of paralysing public transport in the greatest city on earth" and said the United Kingdom was a "world leader in reducing the greenhouse gases that are associated with climate change".
"After leaving four of five locations in good order, rebels will meet at Marble Arch on Monday to decide where they go next", the group said in a statement.
They know a fair bit about extinction at the Natural History Museum but rather less about rebellion.
'Surely this is the time for the protesters to take their pink boat to Tiananmen Square, and lecture them in the way they have been lecturing us'.