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Ketones are the waste product produced when your body is burning fat and protein for energy instead of carbs. Up until lately, being in ketosis has been considered bad, because on low-protein diets, elevated ketone levels mean that you are digesting your own muscle tissue, ie, starving.
On the Atkins diet, producting ketones means that the diet is working and that the fuel source your body is using is the protein you eat and the fat you are losing. (The bad breath is due to ketones leaving your body through your exhalations)
You need to drink a lot of water to flush out the ketones, otherwise, your body will be fooled into thinking you are starving to death, and will try to shut down. This is the feeling of fatigue you get when you first start the diet. Drink water and it will pass.
Before long, the body adapts to using protein and fat for fuel, your insulin levels normalize, and thereby increase your serotonin levels, which make you feel full and happy. The Atkins diet is a great anti-depressant.
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Wait a minute! Where am I, and why am I in this handbasket?
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