The particular incident occurs soon after Daisy had knocked Myrtle down and killed her while driving Gatsby's car. Instead of stopping, she sped away and Jay had to pull up the emergency brake to stop the car and she then fell into his lap. Gatsby then drove her home. After Nick arrives at the Buchanan house with Tom and Jordan, he later sees Jay stepping out of the bushes, intent on spending the night outside the house to see that nothing happens to Daisy.
Nick suspects that Tom might have preconceived ideas if he finds out that Daisy had driven the car, killing Myrtle. He therefore steps around and spies on them through a pantry window.
Tom and Daisy are in deep conversation. Nick comments that:
... anybody would have said that they were conspiring together.
At this point, we can assume that Tom knows what happened and that he and Daisy are planning a way out of the mess. They clearly do not wish to be implicated. This fact is confirmed later in chapter eight when, after Jay's murder by Mr. Wilson, Nick calls to speak to Daisy but is informed that she and Tom have packed their bags and left for some unknown destination, without leaving any contact details or mentioning when they would be back. They literally fled. Obviously, with both Jay and Mr. Wilson deceased, there would be no substantial evidence to implicate Daisy. She and her husband conveniently disappeared.
At the end of chapter 7 of the "Great Gatsby," we find Gatsby and Nick talking in the drive outside of Tom's and Daisy's house. Gatsby indicates that he is concerned for her and Nick tells him to wait while he goes to the house to see if there is any trouble.
I came to a small rectangle of light which I guessed what the pantry window. The blind was drawn, but I found a firt at the sill. Daisy and Tom were sitting opposite each other at the kitchen table, with a plate of cold fried chicken between them and two bottles of ale. He was talking intently across the table at her.....anybody would have said that they were conspiring together.
We of course have no way of knowing what they were saying, but we can assume since he is holding her hand, and they are talking very seriously, that she has indeed told him what happened and Tom is planning how to "spin" the story to their advantage. We know that Daisy is never accused of driving and Mr. Wilson kills Gatsby for revenge because Tom tells Wilson that it was Jay's car that hit Myrtle.