After reading JadeVelcroon’s interpretation, I’ve come with a complementary idea:

From "Number nine out of eleven little littermates..." to "Is after my throne."

• It's clear the explanation that #9 became the most talented assassin of the group and crave for the "throne". It could be literally the throne, the role of ruler, the only one free in this place, as the next lines says:

> "Takes a look at the free world behind the gate Of a castle and escapes."

• It seems that they are not free. The 11 littlermates are servants and #9 escapes to the free world, as he "feels almighty" and wishes for more in his life.

>" I leave the baits, the night awaits"

• 9 went away, but will return to his home. He went to taste freedom, but eventually will return by the night, and the "king" sets a trap for #9, as this kind of quest puts his position at risk.

> "Evaded all but one, one by one."

• Here is where my ideas diverge from JadeVelcroon’s. In this case, the #9 didn't kill the other littlermates, he faced and passed through them, one by one, except for one, the last one.

> "Eleven little litter mates, Annihilate."

• This phrase seems to be the command, the 10 littlemates should kill #9, but he is hiding, evading the others, as it's said through "Only Number Nine's not in sight, Hiding, for the moonlight eats the day".

> "Kisses burn the paper thin wings away" It makes sense that the last one that #9 faced got his attention in a loving way. Her kisses confused his feelings and he realize a weakness.

> "Hate me, hate me, if they want you to break me"

• The last part shows that the last one is acting against the orders. Instead of killing him right away, she is showing him love.

> "Love ? is ? for the weak"

• Again, he reafirms the idea of a weakness.

> And the restless, relief in the end. >A broken lock and a twisted dream >For an early tomb, destiny's overruled >Trailed it back to the Pagan Cathedral."

• After fighting the feeling for a long time (restless), he embraces the feeling (relief), trusting in the last one and the possibility of love (a twisted dream), he was after freedom to begin with, so, trusting that life could be even more is very tempting. They go to a place to spend the night together (the broken lock of the Cathedral). However, something else will happen in this place, one of them will die (hence the early tomb).

>Don't love me, don't you dare! >I lie, I cheat and I don't care >Don't you go telling me tales about fidelity.

• Now she is beyond just kisses and the physical attraction. She's selling the idea that she is loyal to him (justifying why she went against the original order of killing him). But he stills unbelieving in such things (as we know from the beginning, #9 was the best assassin, he has a strong mind).

>In (sane), in (pain) >Ran into a needle >Eye (love), Eye (hate) >Don't need anyone >Lights (on), Lights (out)

• These shows his struggle. In his eyes there is love, but also hate. "don' need anyone" reinforces that he should not fall in love. He should be cold, a tool, as he was trained to be.

>Read it loud and clear >And hear the lion roar. -Here his instincts take over and the feelings win the struggle, he trusts her now.

>Without my eyes, they failed me,

• He doesn't see the things as before, now he believes in love

>Knots untied. >I turned my weakness into a > Fine profession

• They get undressed, he is totally seduced and falls for her charms. Now, as they make love through the night the weakness is turned into an activity.

>More I hear, more I see, I can feel >The path I choose

• The more he experiences the moments with her, more he tastes about this new life, free and with love.

>What I did was a must,

• The desire was too strong.

-In the next lines, #9 realizes what happened and regret his mistake.

>Someone thought to know me well >Drowned me in a wishing well

• He believed in her story about loyalty, love etc. and blinded him through desire and dreams (the twisted dream)

>Making mistakes, we all do, >Worst of mine was trusting in a stranger.

• Here #9 realizes she was a stranger. He didn't really know her, nor did she knew him. But she did convince him and in the end got the job done, as he says

>for now I'm feeling fine >Drank poison, liked the sign Even if he is poisoned and will die soon, he is fine for now ("an early tomb" - early because he won't die from aging)

I'm not sure about the next parts, but it could be that:

>Now touch the greatest fear >Impaired, to look sincere." He realizes the lost and the truth. Early she was swearing loyalty and love, she was willing to leave it all to be with him, so lose him would be "the greatest fear" But since it is all a lie, #9 realizes that she was trying to be convincing, "to look sincere". She was acting all this time and her plan was to fulfill the order and annihilate #9.

The final lines could be through the vision of the girl:

> One step behind you, turn around and I am gone with what I need. -One step behind not physically, but as opposed to "one step ahead". She let him think all along that he was controlling the situation, but it was all part of her plan. He believed, and she finished the job.

> The essence of timely death, cold and dark...

• Here she reaffirms her role as a mercenary, got his guard down and went away with a timely death. Cold and dark, as she used his feelings to get close enough.

>Love Less Hard. -He dreamed too much, and this was his doom.