Archer was dropped from the England side for the second Test against West Indies after it emerged he had broken his journey between the Ageas Bowl and Emirates Old Trafford by making a brief but unauthorised visit to his home in Brighton.
While Archer insists he was only at home for around an hour, he is understood to have had contact with at least one other individual. As a result, he exposed himself and, as a consequence, potentially everyone else involved in the series to an increased threat of the Covid-19 virus.
Archer is currently in isolation in his hotel room at the ground in Manchester. He will not be allowed any face-to-face contact for five days. He is expected to be reintegrated into the full squad the day after the second Test is scheduled to end. The curtains in his hotel room, looking across the Old Trafford pitch, remained closed on Thursday.
Now Giles, the managing director of the England men's teams, says Archer will have to undergo a disciplinary process which could result in a longer absence from the game.
"This could have been disaster," Giles said. "The ripple effect from this small act could have cost us tens of millions of pounds.
"The potential knock on effect I don't think Jofra could have understood. We made it clear what we expected but maybe he did not quite understand.
"There has to be consequence to every action and there will be a process we go through. There will be a disciplinary process. That is as much as I want to say on that as it is an employment matter."
But while Giles was clear that Archer had erred in his judgement, he was keen to record his support for a player he regards as "a great asset to this team". And he made a distinction between the case of Archer and Alex Hales, who finds himself excluded from England's limited-overs squad after a couple of disciplinary lapses. As Giles points out, this is Archer's first such indiscretion.
"That balance with support is equally important in this case," Giles said. "We have all made mistakes. Jofra will learn from this. We will support him and move on.
"I don't think trust is something lost or gained over one incident. Jofra has been around in this team as long as I have. This is the first issue I have had with him. They [Archer and Hales] are different in that.
"Jofra has been a very good addition to this team. He is fine young man, incredibly polite, works hard and is a great asset to this team. On this occasion he got it wrong."
The trip came to light when Archer mentioned it, in passing, to a member of the support staff at training on Wednesday. That member of the support staff felt it was their duty to inform the medical staff and from there matters escalated quite quickly. Some members of the team management were informed at around 10pm on Wednesday night, while the players were informed at 7.50am on the morning of the game.
Archer claims he only saw one other person and they were quickly contacted and tested. The test result was negative.
While the ECB regard the risk of virus transmission as low, they were concerned at the reaction of other touring teams. If any of those sides - not least Australia, who are understood to be on the brink of confirming their tour in September - conclude that the ECB's protocols are not sufficient to ensure the safety of their players, there is a possibility they could call off their tours. That would have catastrophic consequences for the finances of the game in England and Wales.
As a result, ECB officials held conversations with their counterparts at Cricket West Indies, the PCB, Cricket Ireland and Cricket Australia on Thursday. The ECB also contacted the DCMS (the UK government's Department for Digital, Culture, Media & Sport), who sanctioned this series after the ECB satisfied them about their safety protocols and could, in an extreme case, withdraw their support. Nearly 50,000 people have died from the virus so far in the UK and the country is only now gradually emerging from lockdown.
"We have a huge amount of respect for the West Indies coming here and playing this series," Giles said. "And risk jeopardising all of that with one decision. We are responsible and accountable.
"We are asking a lot of the players to stay in these environments for long periods, but it is for good reason. With help from the government and the opposition, these series were set up under these conditions with these protocols and everyone has to abide by them."
There has been some speculation over the policy of players driving their own cars between venues. The ECB insist this was based on medical advice as it avoids the necessity for players to spend hours on coach journeys breathing the same air.
"The advice we had was that it would be safer to keep players away from each other," Giles said. "If there were an infection and you have everyone on a bus, there would be a problem."
There have also been comparisons with the decision to allow Phil Simmons, the West Indies coach, to attend his father-in-law's funeral during this tour. The key difference on that occasion is that Simmons' trip was sanctioned in advance, so his return to the bio-secure bubble was overseen by medics. As a result, he spent five days in isolation and was twice tested for the virus before he was allowed to integrate with the rest of the squad. Archer, by contrast, trained with the squad on Tuesday and could, in a worst case scenario, have exposed them to the virus. Only after that session did his detour come to light.
The identity of the person seen by Archer in Brighton remains unclear. While there has been some speculation that it was his Sussex and sometime England teammate Chris Jordan - the pair live in adjoining flats and are close friends - Jordan declined to confirm or deny the suggestion. Jordan is currently recovering from an operation on his right bicep that could keep him out of the entire season.
"Jofra has demonstrated how sorry he is but it is clearly very disappointing for the whole group," Giles said. "But he is a young man and young men make mistakes. He has to learn from it."