No one saw his fervent pain.
No one saw the anger seething for within.
No one saw a young little boy,
Behind a grown man of sin.

No one dared to touch him,
Out of fear and orderliness.
No one dared to approach him,
And led to lies and faithlessness.

These two stanzas refer to how lost Anakin felt throughout Attack of the Clones and Revenge of the Sith. Although he loves and trusts Padmé, she doesn't exactly understand the situation of the Jedi just exactly how tempting it can be to give into emotions and essentially turn to the Dark Side. Now on top of that, everyone else is just telling him what to do. All of this then led to the exception of Palpatine.

The innocence burns away,
Lava on a soul.
An innocence that burns so great-
His body burns to hell.

Mustafar = burning lava planet. So how fitting that it symbolize hell? The Battle on Mustafar with Obi-Wan seals Anakin's fall to the Dark Side, as he physically and spiritually burns.

A fire hopeless to forgiving rain,
A rain smothered by the flames.
A young little lad and a young little girl,
Force love on their separate ways.

At this point, Anakin is so far gone that even Padmé couldn't have saved him. The "fire" cannot be smothered by the rain. This is the part where Anakin and Padme part ways. Both essentially die –Padmé physically, Anakin metaphorically speaking. Although they loved each other very much, that all went away.

And on a planet far away,
Is you and me and him.
Who knows what tomorrow will bring?
Destiny acts on her own whim.

This is the beginning of Luke's journey some 20 years later on Tatooine where he's just another ordinary guy until fate changes everything.

But one must fall for the other to stand,
Sin passed from kin to kin.
Redemption is far-fetched enough,
To be controlled therein.

Choirs shall sing of a final match,
And the two choices there are to make.
They say no third door will save the day,
And kill he must for our sakes.

In the beginning, there are only two choices presented to the mind of the audience. Either Luke will kill his father or join in and turn to the Dark Side. However, the possibility that such an evil like Darth Vader can be redeemed seems so crazy and impossible, that it just might work. (Ever get into that kind of situation?)

Yet the impossible believe,
And the wretched door to take,
Can change a life, change a view-
And murderous fate forsake.

Luke believes that he can still save his father, that there is still good in him. So we takes that third option in hope to escape what is being asked of him. It works, so who's complaining? :)

For what is a father without his son?
The guiding light doth shine.
Catharsis is a drug we all yearn for,
Tonight with dead armor we dine.
"And please father please,"
Ye call and ye yearn,
"Come back into the Light.
Come back from the fires and lava of hell,
And into the Endor night."

(Rather self explanatory) A short statement on the father/son relationship, redemption and Luke's pyre for his father

[guilt to flames shall burn anew]
[fire to innocence forever renewed]

Just a couplet to finish things off. Anakin's innocence effectively burned away on Mustafar, but now his guilt has ebbed away –if you understand me. What was once fire is slowly giving away to innocence. (Not really, but you understand the metaphor)