Thompson said the ASADA-led investigation was the most serious and difficult situation he had encountered during his time in football, admitting he was shocked when the need for an investigation became apparent.
"In all honesty it is a challenge. It is something we have to get through because we have to play games of footy and we have to win our respect back to our members, to sponsors, to the game, to everybody," Thompson told AFL 360.
However he said the club was prepared to accept the difficult situation in order to discover the truth.
Thompson said that things changed every day but the club was bringing people together and discussing the issue continually in order to navigate their way through the ordeal.
He said Essendon players had been good given the circumstances and once they were out on the track they found it to be business as usual. It was when the footballs were put away that everyone was reminded of the club's predicament.
"We've all found it difficult," Thompson said.
"It's been very hard to survive and to live. Everywhere you go you feel embarrassed and you think that people are thinking that you have done these things that everyone has been saying we have been doing but to be honest we just have to sit back and wait.
"We can't defend ourselves because we are not allowed to.
"We understand that we are part of this process and we want to find the truth out. Once the truth comes out then we will deal with the consequences."
Thompson conceded that the club was exploring new territory in 2012 and said there was "obviously some risk involved".
Despite the risks, Thompson said he was shocked when Essendon found itself in the position to have to request for ASADA to investigate the club.
