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The Internal Block Diagram (IBD) shows the 3 main headers with all «pin» Ports and all nested logical contract Ports, as well as ICSP headers for each of the ATmega2560 and ATmega16U2 chips, in the context of the Arduino Mega2560R3 board.
No specific connections are shown (yet), we'll see those in dedicated smaller diagrams according to function groups and (where appropriate) also with the chip pins. One can however see for many pins as Context-Specific Values (in the not so ideally named initialValues compartment) the pin mappings to the main ATmega2560 mcu chip and the ATmega16U2 chip (used for USB-to-TTL), as gleaned from the official Arduino pinout diagrams.
The nested logical contract Ports show where specific "logical" connections could be made to represent use of specific functionality for pins with overloaded functionality (as would usually be driven by Arduino library commands for a specific application). These won't be used further in this trail.
This tool feature was used again: