The quote you have identified comes as part of what Rousseau tells the speaker about his existence of life. It is always worth considering the quote in full before trying to establish its meaning, and here are the lines you have indicated in full:
The world was darkened beneath either pinion
Of him whom from the flock of conquerors
Fame singled out for her thunder-bearing minion;
The other long outlived both woes and wars,
Throned in the thoughts of men, and still had kept
The jealous key of Truth's eternal door,
If Bacon's eagle spirit had not lept
Like lightning out of darkness--he compelled
The Proteus shape of Nature, as it slept
To wake, and lead him to the caves that held
The treasure of the secrets of its reign.
This section of the poem comes as Rousseau, who acts like Virgil does for Dante in his Inferno, guides the speaker through the visions he is seeing of the triumph of life. Having seen and explained the host of important figures who are in the procession of life, Rousseau then goes on to refer to the role of Satan and Jesus in representing two conflicting systems of control in our lives. The reference to Nature at the end of the quote again refers to the speaker's desire to find out the meaning of life and how it should be led.
i think that the two persons that the poet isreferrign to are still Alexander and Aristotle.
while one was a conqueror the other ( Aristotle ) being a philosopher lived on in the thought of men, but still did not share all his knowledge.
This was done by Bacon whose eagle ( knowledge) opened the doors for others.