Former High Court judge, Sir Michael Wright, began summing up seven weeks of evidence by telling jurors they will only be allowed to return a verdict of lawful killing or an open verdict.
Having considered all the evidence, a verdict of unlawful killing was "not justified", he said.
The coroner told jurors to cast aside "any emotion" over the innocent Brazilian's shooting.
He also warned the 11 jurors they must not attach any criminal or civil fault to individuals.
He told them verdicts cannot be inconsistent with the outcome of the Metropolitan Police's health and safety trial, which spared Deputy Assistant Commissioner Cressida Dick of personal blame.
Reminding the jury that the Brazilian's mother, Maria Otone de Menezes, had seen much of the evidence, the coroner added: "I know that your heart will go out to her.
"But these are emotional reactions, ladies and gentlemen, and you are charged with returning a verdict based on evidence.
"Put aside any emotion - put them to one side."
The coroner began bringing together the final account of how the innocent Brazilian met his death on a south London Tube train.
It is the last stage before the 11-person jury, which has sat since September 22, is sent out to consider its verdicts.
Jurors heard from 100 witnesses, including the two men who shot dead the innocent Brazilian at point-blank range on a carriage at Stockwell station on July 22, 2005.
For the first time, the public was given a full account of the incident from key witnesses on board the Underground carriage where the shooting took place.
Key controversies involving surveillance outside his Tulse Hill home, incidents in the control room at New Scotland Yard, and Mr de Menezes's journey towards Stockwell were also examined at length.
C2 and C12, the two firearms officers who shot the electrician, both choked back tears as they appeared in the unlikely surroundings of Surrey County Cricket Club's home ground, in south London.
The shooting came two weeks after London was rocked by the July 7 bombings that left 52 victims dead.
On July 21 a second gang of Islamist extremists attempted to murder dozens more with home-made rucksack bombs.
As counter terrorist police scoured the capital for the escaped would-be suicide bombers, Mr de Menezes was mistaken for one of them and shot dead.
Sir Michael is expected to use at least two days taking the jury back through the key evidence heard at The Oval.
In addition to the two verdicts available, jurors will consider a series of questions, the coroner added.
He told them they should answer "yes", "no" or "cannot decide" to the following questions:
* Did C12 shout the words "armed police" before opening fire?
* Did Mr de Menezes stand up from his seat before he was grabbed in a bear hug by Ivor?
* Did Mr de Menezes move towards C12 before he was grabbed in a bear hug by Ivor?
* Which factors led to his death?
a) The pressure on police after the suicide attacks in July 2005.
b) A failure to provide better photographic images of failed bomber Hussain Osman to surveillance officers.
c) A failure by police to ensure that Mr de Menezes was stopped before he reached public transport.
d) The general difficulty in providing identification of the man under surveillance in the time available.
e) The innocent behaviour of Mr de Menezes increasing suspicion.
f) The fact the views of the surveillance officers regarding identification were not accurately communicated to the command team and firearms officers.
g) The fact that the position of the cars containing the firearms officers was not accurately known by the command team as firearms teams were approaching Stockwell Tube.
h) Shortcomings in the communications system between various police teams on the ground.
i) Failure to conclude at the time that surveillance officers could have been used to carry out the stop on Mr de Menezes at Stockwell.
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