He will learn his fate before then, with England likely to punish him, although they know it is a fine balance between laying down the law and being understanding of players living in a suffocating biosecure bubble.
He is missing this match but that is for medical protocol reasons, and not as punishment, and Giles will decide whether he should be suspended for the final Test of the series.
England feared the nightmare scenario of Archer having been infected with coronavirus, which would have put in doubt the rest of the international summer following warnings the game would incur £380million ($NZ730m) in losses if England could not fulfil their fixtures.
"There have to be consequences to every action and there will be a [disciplinary] process we go through," Giles said. "This could have been a disaster. The ripple effect of this small act could have cost us tens of millions of pounds. The potential knock-on effect, I don't think he could have understood. We made it clear what we expected but maybe he did not quite understand."
Friends were quoted on Thursday night as saying he went to see his dog, that he shares with fellow England player Chris Jordan. Giles refused to comment on whether Archer had gone to see his girlfriend or the circumstances of his trip home.
"Everyone was aware of what we were asking of them and why. In normal circumstances the act of going home between matches is normal, but clearly a lot of work and money has gone into setting up this biosecure environment and there a lot at stake: This match, this series, this summer and financially things much bigger beyond that," Giles said.
"Jofra has demonstrated how sorry he is but it is clearly very disappointing for the whole group. He is a young man and young men make mistakes and he has to learn from them."
"There will be a disciplinary process to go through. That is as much as I want to say on that, it is an employment matter. We will settle that in good time."
England learned of Archer's 130-mile detour to his flat when he admitted to a member of the backroom team that he had gone home on the way to Manchester. That individual alerted the England management, who told the medical staff. Giles was called late on Wednesday night and then made Tom Harrison, the England and Wales Cricket Board chief executive, aware of the situation.
The board spent Thursday morning (UK time) trying to reassure governing bodies and the Government that they were in control of the situation. There were talks with the Department for Digital, Culture, Media and Sport, which gave permission for the series to go ahead on the proviso of strict biosecure conditions. The ECB also scrambled to contact officials at Cricket Ireland, Cricket West Indies, the Pakistan Cricket Board and Cricket Australia to reassure them that its Covid protocols were secure. Pakistan are already there, Ireland arrive next week for a one-day series and talks were due on Thursday with CA to finalise the itinerary for a one-day series in September.
The rest of the squad were summoned to a team meeting at 8am on Thursday to be told the news, although some missed it because they were asleep when the message was sent by Phil Neale, the logistics manager, telling them to go to the team room.
All the players, including Archer were tested at the Ageas Bowl on Monday afternoon. Some stayed on to play golf. They travelled between Southampton and Manchester in their individual cars. They were given guidance on what to do if they had to stop on the way but not specific places to go. They were given a set time to arrive at Old Trafford on Monday night. All of them, including Archer, arrived on time.
They were all reminded verbally and on Whatsapp groups about the instructions for travelling between venues, which was identified as the most vulnerable part of the ECB's plans, and a reminder was given before they left Southampton.
The West Indies travelled in a fleet of buses because one coach could not fit all members of the team and staff for social distancing reasons.
But the ECB believes individual cars are safer because sitting in an enclosed bus with recycled air is seen as risky. Part of the guidelines given to county players is to travel in their own vehicles. However, it places the burden of responsibility on the player, and a level of trust that Archer has breached.
The team doctors are in communication with Archer and he will be offered mental health support if he needs it while isolated in his room. Meals will be delivered to his room and he will have two Covid tests that will both have to come back negative before he is able to rejoin the group.
It is understood that if he had asked for permission to go home it may have been granted, with a doctor accompanying him and steps put in place to test him afterwards.
"I am extremely sorry for what I have done," said Archer in a statement. "I have put, not only myself, but the whole team and management in danger.
"I fully accept the consequences of my actions, and I want to sincerely apologise to everyone in the bio-secure bubble. It deeply pains me to be missing the Test match, especially with the series poised. I feel like I have let both teams down, and again I am sorry."
- Daily Telegraph UK