5. When a server was installed and 
     switched on, the microchip altered 
     the operating system’s core so it 
     could accept modifications. The chip 
     could also contact computers controlled 
     by the attackers in search of further 
     instructions and code.

So, in typical vulnerability/payload/exploit fashion, the board's bus is vulnerable by default, because the chip pierces all the usual lines of defense protecting against network and operator I/O. It carries a payload intended to target very common features used everywhere commodity servers are used, one that likely listens for DMA traffic on the bus, and alters the signal stream, by escaping upon the occurrence of a magic sequence, and inserting its own signal, before resuming the authentic stream in flight.

The payload could be pretty small, since the server boards are likely using OS packages that match the chipset. This limits the software to a small set of well known targets, Linux, Windows, Apple. Target their kernels, and you only have to snip out a small chunk of bytes, and splice your own pre-defined package in. Splice in a miniature runtime, that operates a turing complete set of operations, and open up a listener that waits for network access, and now, your payload can enable arbitrary code execution, irrespective of permissions.

Now, to exploit, the payload needs to time the opportunity to splice itself onto the disk correctly. If certain well-known chunks of code will always exist in each given operating system, then with every disk access event one just needs to wait for the inevitable moment those magic system-specific bytes travel over the bus, in order to replace the known bytes with the poisoned modification. Events might target when the bytes are originally installed with the OS, or every time the OS reads those known bytes back into live memory, from any source.

The total payload package could probably fit inside a couple of megabytes, pack on a few more for the "listen & splice" part of the attack to round out the entire mass, and all we know how much data an SD card can fit into say... five grains of rice?