Atonement may seem an odd word to associate with Buddhism. In other religions, atonement is associated with repentance for sins and making peace with God, which doesn't sound very Buddhist. Buddhism has its own kind of atonement, however.
Back in the 16th century the English word atonement meant something like "condition of being at one" with something or someone, according to an online etymology dictionary. The word later evolved to mean making amends or appeasing, but here we're going with the original meaning -- at-one-ment.
All evil karma ever committed by me since of old,
Because of my beginningless greed, anger, and ignorance,
Born of my body, mouth, and thought,
Now I atone for it all.
We have to be "at one" with evil karma? Teachers say that acknowledging and taking responsibility for harmful actions is a necessary part of purification. And this is more than just an admission of personal shortcomings. To be at one with all evil karma is to be at one with the truth of suffering (dukkha) of all beings. Karma is created by body, speech, and thought.
This atonement also is a positive declaration that we are at one with the life of all beings. We are not separate from anything. In this way atonement gives rise to compassion. This is how atonement works from a Buddhist perspective.