[W]hen the blood is fresh, the spirits pure and vigorous, not only to vital, but to rationall faculties, and those in the acutest, and the pertest operations of wit and suttlety, it argues in what good plight and constitution the body is, so when the cherfulnesse of the people is so sprightly up, as that it has not only wherewith to guard well its own freedom and safety, but to spare, and to bestow upon the solidest and sublimest points of controversie, and new invention, it betok'ns us not degenerated, nor drooping to a fatall decay, but casting off the old and wrincl'd skin of corruption to outlive these pangs and wax young again, entring the glorious waies of Truth and prosperous vertue destin'd to become great and honourable in these latter ages. Methinks I see in my mind a noble and puissant Nation rousing herself like a strong man after sleep, and shaking her invincible locks: Methinks I see her as an Eagle muing her mighty youth, and kindling her undazl'd eyes at the full midday beam; purging and unscaling her long abused sight at the fountain it self of heav'nly radiance; while the whole noise of timorous and flocking birds, with those also that love the twilight, flutter about, amaz'd at what she means, and in their envious gabble would prognosticat a year of sects and schisms.
The passage from Areopagitica that includes the metaphors in question is one in which John Milton is saying that a city besieged [and here he means besieged in a metaphysical metaphorical sense, not a literal physical sense] can withstand and rise up victorious if her people have been in the "study of highest and most important matters" and have been "disputing, reasoning, ... discoursing" to an extent never before known on things of the greatest importance because such lofty pursuit of the highest ideals leads to people of "singular good will" who have "gallant bravery" and just "contempt of their enemies," who in this discussion are metaphysical concepts that war against "highest and most important matters."
When Milton gets to the "Methinks" metaphors, he is enlarging upon this discussion and paining an image of what such a nation would look like and how other nations would react to her because of "the glorious waies of Truth and prosperous vertue." Firstly, he sees a "noble and puissant [powerful, mighty] Nation" awakening from a deep sleep--a sleep caused by neglect of the "highest and most important matters" in a metaphysical realm of "Truth and ... vertue"--like a strong man who shakes his "invincible locks," which is a Biblical to the strength of Samson, before he was despoiled by Delilah. Secondly, Milton sees this "Nation" as "an Eagle" who is "muing," or molting from youthful feathers to expose the feathers of full adulthood and looking unscathed with her keen eyes straight into the midday sun, which is another Biblical allusion to the Judaic God and His splendor, and in the "heav'nly radiznce thereof cleansing and purifying, or "purging," her "long abused sight."
Thirdly, Milton sees the other flocks of birds, which represent the other nations--who are lovers of "twilight," meaning they reject the purifying radiance of midday sunlight--fluttering and squawking about while they "eviously gabble" about gloomy prognostications (i.e., predict, foretell) and false prophesies, as it were, of religious schisms and the development of dissenting sects that bespeak disunity and petty squabbling, which would be the opposite of the image Milton just painted.