"Unfortunately, throughout my tenure, various events have gradually made it impossible for me to carry on," said Rush.
"The club's decision to terminate the contract of my assistant, Mark Aizlewood, without my consent was the final straw."
Following the departure of Aizlewood on Monday, Rush has now decided to resign.
"I was already considering my position after the much publicised comments from the club a few weeks ago," Rush added.
"Loyalty is vital in football and I am a loyal person. When a valued member of my team is dismissed against my wishes, I have no option but to follow my principles."
Rush's appointment in August saw an immediate good run for Chester Rush was named League Two manager of the month in August.
However a disappointing slump in the New Year meant Rush's job came under threat in March.
A somewhat bitter Rush commented on the apparent slump in form which led to talks of him being paid off.
"Since I came to
"We have steered the club, slowly but surely, away from the foot of the table - where it was when I joined. The club is a good nine points away from relegation.
"People talk of a slump but how can you slump from the foot of the table to nine points clear of relegation?"
Rush is now looking to getting back into football with his team as soon as possible.