With flying colours
Ships serve scientific and cultural needs, as well as the transportation of goods, and resolving political and national conflict. In the past, without the use of modern communication devices, a ship's appearance upon the immediate return to the port could communicate how the crew fared at sea. Ships that were victorious in their endeavours – e.g. an encounter with an enemy ship – would sail into port with flags flying from the mastheads. On the other hand, a ship that had been defeated, if still afloat, would be forced to "strike her colours", or to take them down, signifying her defeat. Although the time period is estimated roughly into the Age of Discovery, prior to the 18th century these phrases were used solely as nautical terms, and afterward they began to be used in the vernacular figuratively to signify any kind of triumph. Also, another phrase, "go down with flying colours" or "go down with colours flying" was used to express a commitment; in other words, a resolute crew fighting, even until their ship sinks. A variant of this phrase gives virtually the same meaning, "Nail your colours to the mast". If the colours, or the flag is nailed onto the mast, it cannot be lowered. There is effectively no way to express submission.
The word colours as used in the phrase historically was an alternative to saying flag, particularly to display a party's affiliation or allegiance to a nation. The calling of the flag as colours may of course, have non-nautical phrases as colours was used to express patriotism and nationality; other such examples of phrases being "true colours", or "show your colours". Flying, of course, refers to the unfurled flags' position on the masthead, and the variants come off or pass simply mean to have returned from the sea and to pass into the harbour, respectively.
Similarly, the phrase "sailing under false colours" was a reference to a tactic used by pirates or maritime robbers roaming the seas to attack vessels with desired booty. By hoisting a friendly flag, the unsuspecting ship would allow the pirates' ship to approach without resistance, giving the pirates access to board their vessel. Blackbeard famously repeated this process for two years, and sometimes upon sight of their ship, with a pirate flag replacing the deceptive friendly one, the ship would immediately surrender. However, this was not limited historically to pirates, as the British Royal Navy had used this tactic when chasing Bartholomew Roberts.
These phrases have been used many times in literary works, even in modern-day writings. "With flying colours" has many variations preceding it, such as to pass..., came out..., and came through..., but all have the same meaning derived from the literal allusion, to be triumphant or victorious, honorable or to be publicly successful. "Go down with colours flying" and "Nail your colours to the mast" are used similarly to the nautical allusion, and are phrases to express persistence or stubbornness.
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- The dictionary definition of with flying colours at Wiktionary