Before I begin my alternative ending a few ideas have to be explained and added to the original story as well as explaining why I'm doing this.

If you think about the original ending it becomes clear that, in the end, what you have done is completely useless: the bioshock infinite universe maintains that every choice causes new alternate dimensions to be created but it seems the random chances within each universe remain the same (the coin toss for example) this means that at the end when Elizabeth decides to kill Booker before he goes to be baptised to stop Comstock from existing, and herself, there is an alternate dimension in which she didn't decide this and therefore Comstock still survives in infinite forms. Even if you accept because she's a time dimension goddess and did some crazy magiks to make it so that couldn't happen, there would be someone who was like Comstock who created Columbia and everything still happened. Also why focus on stopping this one event? If infinite dimensions exist then infinite bad events happen in infinite locations and it becomes a big mess. One big meaningless mess. Because Elizabeth drowning you achieves nothing, except the death of your character and the non existence of that form of Elizabeth you've spent the entire game becoming emotionally invested in: leaving a sour and depressing taste in the mouth. All pointless,all meaningless.

So what I think would be a acceptable ending requires some tweaks to the main story but would essentially keep the core intact.

The universe has not always had multiple dimensions but only one time line going from beginning to end. This time line is the one where Booker did the baptism and became Comstock and because of that he met the female Lutece who then invented the ability to create tears but what she actually did was shattered the universe's time line into infinite possibilities and only realises after being scattered across space and time.
However before they realise this mistake they've already taken Anna, and tried to send Anna back and their consciousnesses (which are the combined consciousness of all the male and female Lutece's in 2 bodies due to being scattered across space time) has been thrown into a between state of being here but not (not able to fix their mistake due to being unable to approach the device). They need the help of someone and decide on Booker due to taking his child running on the pretence as before in the game.
Booker does everything he's meant to do but throughout the game voxboxes are left to hint at these possible discoveries as well as dialogue between the eccentric "twins". Also it should be noted that

both Booker and Elizabeth of the universe the player is in are dead – Booker is dead as a martyr and I theorise that since Comstock took Elizabeth to be experimented on until she accept his philosophy and become his heir then either this universe's Elizabeth is dead or wasn't there to begin with or something similar. Why else would he take if he already had one?

And now without further ado, I present my ending from booker's point of view:

I blow the haunting melody that commands the song bird, willing the monster to attack the siphon inside the statue that encloses it. It rises up in the distance above the statue, with its shattered neck, before diving inside and a moment later a great explosion of glass, the right arm falling away, a great plume of blue light bursting into the air followed closely by what I can only describe as whumpf roaring noise. A second explosion of glass and more bursts of the blue light, the whole statue destroyed as a great explosion of blue light and crackling energy bursts out engulfing myself and Elizabeth. I look at my hands seeing small blue lines of crackling electricity around the organ whistle, an expanding white light filling my vision as I drop the instrument and suddenly I black out.

My eyes open slowly, blinking in the white that surrounds me. For as far as I can see white. Below me white. Everywhere white and yet I stand on it, in it. I suddenly look around this way and that crying out.

"Elizabeth! Elizabeeeeeeeeth!"

"She's not here you know"

The female voice behind me startles me though familiar. I turn and there standing are the Lutece's.

"Wha..what do you mean? Where is she? Where is she!?" I exclaim, looking frantic at the two people before me, calm and composed.

"You are not there" Rosalind replies

"She is not here" Her 'brother' adds

"I" Rosalind begins

"We" injects Robert

"Us" She starts again "Have a lot to thank you for Mr Dewitt. You have, without your knowledge, fixed.."

"Everything" He brother finishes her sentence "You see there used to be one universe, then there were many, and now there is one again"

"I...I..I don't understand" I mumble groggily my head beginning to spin. I fall back to sitting on the ground my vision blurring as the voices fade.

"I hope, Mr Dewitt, you find"

"Redemption"

I awake to the sound of pounding on a door. Looking around to get my bearings I find myself in the mess of my dishevelled office.

"Mr Dewitt. Bring us the girl and wipe away the debt" A voice shouts through the door. Confused I stumble towards it. A baby begins to cry somewhere close, I turn around to see a door in the corner before turning back to find a man standing before me.. He.. he seems familiar. I know what I have to do. I turn towards the crying and the door. Slowly, I walk step by step towards it, seemingly taking forever but my hand clasps around the doorknob turning it to open the door. Inside the squalid little room there is only a plain wooden crib. A single sheet draped over both sides. The crying emanates from inside, pulling at my heart. I go to the crib and see, lying there a baby. Blue eyed, black haired and wrapped in nothing but blue cloth around her legs, she is the vision of beauty. I reach out with trembling hands and lift her gently, cradling her in my arms. She stops wailing, looking up at me with those bright blue eyes I will never forget.

"Give us the girl and Mr. Comstock will clear the debt, Mr. Dewitt. There's not much time" I look up. The man stands in the door cool and composed, his British accent tweaking my memory. I look back to Anna.

"Anna.. I'm sorry. I'm sorry" My eyes glass over with the formation of tears as I hand her over to the man "I'm sorry..."

"The debts paid. Mr Comstock washes you of all your sins"

Lightning flashes

I'm in an alley way and its pouring with rain, thunder rolls above me and the sky is lit by lightning. Ahead standing in a flickering light from a strange circle on the wall two men stand. The one closest to the circle has his arms cross and I recognize him as the man who took Anna but the other man is the one holding her protectively in his arms. He is about my height, dressed in a fine black suit with cape, thick brown hair combed back with a great thick combed brown beard. I cry out stumbling towards them.

"Hey..Hey, the deal is off! Do you hear me? The deal is off! Give her back."

I hear a distorted female voice saying something reassuring but my concentration is solely on the man holding Anna.

"Give her back!"

I rush forward while the two men hurry through a strange hole on the wall that has a glowing rim around the outside, to a grey room beyond and a woman standing gesturing for the men to hurry. I grab the bearded man's arm as he is stepping through the circle, pulling at him, trying to pull back Anna all the while screaming to give her back.

"Shut it down now! Shut it down, shut it down!" The bearded man shouts and as the circle begins to close he manages to wrench free form my grasp and I stumble backwards. Time seems to slow. The circle gets smaller, the man disappearing, pulling through Anna, her eyes light up blue as lighting cracks the sky, I reach out for her and she reaches out back but the circle closes in around her severing her little finger.

"Give me back my daughter!"

Lightning flashes

I'm standing in a pool of water, surrounded by small grass covered hillocks. Before me stand a semi-circle of people dressed in country clothes, hands clasped under their chins and heads bowed, around an older man. A priest. He too has his hands clasped under his chin and head bowed. I remember this. I came to be baptised but I never went through with it, being dunked doesn't bring redemption, it doesn't wash away the past.

The preacher raises his head and calls out to me "Are you ready to have your past erased? Are you ready to have your sins cleansed? Are you ready to be born again?"

My lips move of their own volition, my voice comes out but I didn't speak the words.

"Yes"

My legs take me forward and the priest extends his hand.

"Take my hand"

My hand takes his hand and he gently pulls me around

"Are you ready to be born again?"

"I am"

"Do you hate your sins?"

"I do"

"Do you hate your wickedness?"

"I do"

"Do you want to clean the slate, leave behind all you were before and be born again in the blood of the Lamb"

"Yes!

"Jesus, wash this man clean.. Lord make him born again. What name shall you take, my son?"

"Zachary Comstock"

I am plunged into the water and then, darkness.

I'm not Zachary.. I'm... Booker... Booker.. "Booker!"

My eyes shoot open at the sound of her voice calling me, her eyes shine bright blue in her beautiful face.

"Anna..?" I whisper, dazed and confused. "Elizabeth?"

"Booker are you all right?" She has her hands on my shoulders as I'm sprawled on the deck. Memory comes back of where I am, as the ship jolts violently and I black out once more"

The eerie sound of the melody filters in as I open my eyes briefly to see the songbird land on the deck next to Elizabeth who points to me. Blackout.

I come to consciousness once more the night sky lit by fire, the airship nowhere to be seen with myself and Elizabeth cradled in the arms of the song bird, its wings beating regularly. Elizabeth is staring off into the distance, her eyes streaming with tears as she does the motions of opening a tear but nothing happens. She cries out her voice wrought with frustration

"Why won't it work!? Why can't I save them!?" She attempts again, concentration filling her face as my eyes move to where she is looking. The night sky is suddenly lit brighter as a massive explosion comes from one of the platforms engulfing it in flames as it beings to lean and fall form the sky. Then another. I can see others already descending down through the clouds.

"Gaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaahh!" Elizabeth screams out as once again, I black out.

"Booker.. Booker" I hear her sweet voice in the darkness fading.

I feel wind on my face. I wake up and find we're flying through the cloudless sky over a vast ocean. Elizabeth is asleep beside me. My head is pounding and I still find myself dazed. I slip once more into darkness.

I hear the soft sound of small waves. I open my eyes slowly to see a sparse sandy shoreline at dusk, myself lying on the sand. The red sun low on the horizon, two figures, one much larger than the other with large wings folded up, are shadowy against it. I hear her voice quietly.

"I'm sorry, I'm here. It's ok. It's all right... Just let go.. Shhshhshh.." She comforts the songbird as it turns and descends into the deep.

"Elizabeth.. I'm sorry" I whisper

Black out to credits

After Credits Epilogue

I close my leather suitcase on my bed, close it with the metal clasps and sigh.

"I suppose its time to go. I'll get the tickets then see if she's ready" I look around the room, a simple blue painted room with a set of drawers, dresser and bed. I open the door to the living room and hear her sorrowful voice singing from he closed room.

Will the circle be unbroken
By and by, by and by?
Is a better home awaiting
In the sky, in the sky?

As the song flows over me, my eyes start to water. She always moved me so with that song. That time in the cellar in Columbia to now. The melody and words bringing back sad memories, of redemption to be had. I walk to the small low table in front of the couch. The tickets there on top of some newspapers with the headlines in French.

Plus découvertes de la catastrophe de Columbia!

Colombie rapatriés aux États-Unis d'Amérique!

And next to a leaflet for the Dewitt Foundation for Civil Rights. I smile, taking it and the tickets reading them: Le Havre to New York. I tuck them into my coat pocket, walking to the door where the sad singing is coming from. I knock gently.

"Are you ready?" I call out and the singing is briefly interrupted.

"Yes father"

Fade to black

Authored by Sciffy