Solution: RC1001 Maritime Communication

Answer: EL CAPITAN

This puzzle presents solvers with a series of lines of boxes, connected by lines. Solvers might intuit (and indeed most did) that boxes connected by lines must contain the same letter, but this observation alone won't get solvers much progress, since many letter patterns are quite ambiguous.

The next jump to make comes from the flavor text's mention of "friendship" and "ship": one might realise that each word in the puzzle can have the word "ship" appended to it to create a new word. This disambiguates some of the words: for example, the third line's xAyyLE can be uniquely identified as BATTLE, as opposed to some other word like BAFFLE or DABBLE.

After filling in all the words, the letters from the 9 boxes with numbers in them can be arranged in order (either by number or color) to spell out the final answer EL CAPITAN.

Here's the diagram, when fully filled out correctly: