In this farewell - referring to when L dies in front of Light.
There’s no blood - referring to how L does not die from a loss of blood or anything of the sort.
There’s no alibi - referring to how everyone thinks Light killed him, when he didn't.
‘Cause I’ve drawn regret - how L regrets ever inviting Light into the Task Force.
From the truth of a thousand lies - mushed together it means that everytime Light lied, there were truth in his words.

[Pre-Chorus:]
So let mercy come - it almost seems that Light was begging for mercy when he turned into a desperate madman on the last episode.
And wash away - the blood from Light's gunfhot wounds washing away into the river.
What I’ve done - obviously, what Light has done being Kira and so forth.

[Chorus:]
I'll face myself - Light facing the second Kira, Misa, who is basically another version of himself.
To cross out what I’ve become - when Ryuk wrote down Light's name in the Death Note, perhaps he wanted to cross out his name.
Erase myself - when Ryuk temporarily erases Light's memories.
And let go of what I’ve done - same as the pre-chrous line.

Put to rest what you thought of me - mushed together it refers to how Light was extremely distrusting of L at the beginning.
While I clean this slate - how Light hides the Death Note to hide it from people. In other words, he wants to clean off his killing spree and eliminate all evidence.
With the hands of uncertainty - how Light is unsure of whether to use the Death Note or not at the beginning.

[Pre-Chorus]

[Chorus]

For what I’ve done - same as the pre-chorus line.
I start again - after Light got his memories back, he was Kira again.
And whatever pain may come - how Light is willing to sacrifice everything for the sake of himself.
Today this ends - refers to when Light dies, when the Kira killings are finally finished.
I’m forgiving what I’ve done - on the last episode, Light finally forgives himself on all the terrible things he has done. Perhaps Misa and Mikami have forgiven him.

[Chorus]

What I’ve done - same as the pre-chorus line again.
Forgiving what I’ve done - this is now how L wishes he could have forgiven Light.