The 39-year-old French film producer was beaten to death on a freezing night outside her holiday home near Schull, west Cork.
Mr Bailey denies any involvement in the killing.
"What is left before you is the issue that has been here from the very beginning - that the Gardai framed Ian Bailey. It is the centrepiece," the judge said.
"You are not actually asked to decide if Ian Bailey committed this dreadful crime. You are also not asked whether (witness) Marie Farrell's statements are true or not."
Ms Farrell made a statement to gardai in the early part of the murder inquiry placing Mr Bailey near the crime scene on the night of the killing but subsequently retracted it and gave evidence on Mr Bailey's behalf.
The jurors have been told to examine two key questions to determine the outcome of the lawsuit.
One is whether three gardai - Detective Jim Fitzgerald, Garda Kevin Kelleher and Detective Jim Slattery - conspired to implicate Mr Bailey in the murder of Ms du Plantier (above) by coercing witness Ms Farrell using threats, inducements or intimidation to make a statement placing Mr Bailey at Kealfada Bridge, near where the murder took place.
The second is whether there was a conspiracy by detectives Mr Fitzgerald and Maurice Walsh to get false statements from Ms Farrell that Mr Bailey had intimidated her.
The state denied all claims.
Judge Hedigan said the legal issue in the case for the jury to decide was "mercifully very limited".
"David and Goliath comparisons can be a little misleading. Be careful of that," he told the jury. "It's important - Goliath has as much right to justice as little David has.
"There are after all, as you have seen, real people on either side of this particular case.
"Ian Bailey says the Gardai tried to frame him and he has put forward Marie Farrell to testify as to how they did that."
The jury was told that the Gardai have rejected that claim.
"Their case is that she is an untruthful witness whose evidence should not be relied on by you," the judge said.
Judge Hedigan told the jurors that they could return a majority verdict on which nine of them agree.