The "check engine" light on my 2000 S500 came on. The scanner says it's a "Secondary Air Injection System Malfunction". What does this mean?

 

There is an electric pump on the front of the engine that injects extra air (oxygen) into the exhaust manifold in order to reduce emmission levels at certain times in the warmup cycle.

Whats the code number?
Could be as simple as a fuse but more likely the pump fails the prestart circuit checks (bootup) for some reason.
Stuart

 

P0410
Also, when I start thecar up in the mornings, there is a rumbling sound by the engine while the car is warming up...then it goes away after a minute or so.

 

Fuse is f31 located (40AMP 3rd fuse back in the big black box at rear of engine compartment ON RHS)

Rumbling noise most probably means that the pump is working but is damaged in someway hence the code.

The pump is a black plastic motor looking thing (transversely mounted) at the fromt of the engine immediately beneath the pull off plastic engine shroud / air filter.

Looks like you need a new one or possibly you could dismantle and examine/repair.

Stuart.