If the data IS related it is your job to ensure that the information is passed along. MapReduce breaks up the data and processes it regardless of any (not implemented) relations:
Map just reads data in blocks from the input files and passes them to the map-function one "record" at a time. Default-record is a line (but can be modified).
You can annotate the data in Map with its origin but what you can basically do with Map is: categorize the data. You emit a new key and new values and MapReduce groups by the new key. So if there are relations between different records: choose the same (or similiar *1) key for emitting them, so they are grouped together.
For Reduce the data is partitioned/sorted (that is where the grouping takes places) and afterwards the reduce-function receives all data from one group: one key and all its associated values. Now you can aggregate over the values. That's it.
So you have an over-all group-by implemented by MapReduce. Everything else is your responsibility. You want a cross product from two sources? Implement it for example by introducing artifical keys and multi-emitting (fragment and replicate join). Your imagination is the limit. And: you can always pass the data through another job.
*1: similiar, because you can influence the choice of grouping later on. normally it is group be identity-function, but you can change this.