Don’t get me wrong. Alfred does care for the boys the Bruce calls his sons, but his devotion is to Bruce first and always. There is a careful balance that Alfred is able to maintain where Bruce’s morality keeps Alfred from going too far in his name. 

Until Jason Todd dies. Jason’s death broke Bruce and in anguish Bruce called out for his dead son. 

Ok, Alfred thought, if Bruce wants his son Jason, then Jason he shall have.  Alfred quietly arranges Jason’s body to be buried in the main cemetery without ceremony. Then he goes to look for a child. Alfred did not need to look farther than next door, to little Tim Drake, who looked enough like Jason that he could pass as Bruce’s missing son and whose parents would be out of the country for another eight months.  Alfred is exceptional at planning and within three days has abducted Tim (with a false trail carefully laid out that lead to Tim’s nanny killing him and then herself- Alfred did regret having to take the woman’s, and another child with a similar build as Tim,  life, but needs must) and encouraged a delusion in Bruce that Jason never died, but instead was hiding from Bruce because of Garzonas. Alfred also instigates a fight between Bruce and Dick that drove Dick away, carefully feeding the fire of Dick’s anger so that he would not come back (because Dick was not broken by grief and would realize that Tim is not Jason-Dick and most of the superhero community do know that Jason died, but next to no one knows that Jason Todd did). 

Within six months Tim has accepted, read been tortured into accepting, that he is to be the replacement Jason Todd (Alfred was careful, Tim did not believe he was Jason because the goal was always to give Bruce his Jason, which means that Tim had to be aware to adjust his behavior accordingly).  During this time Alfred has also made sure that Tim was informed his parents were aware that he was gone but that they were not looking for him, leaving out the part where they thought he was dead. Alfred has trained him thoroughly to be both Jason and Robin. Alfred has also arranged to have Tim/Jason home schooled (because Jason loved school but Tim going in Jason’s place would be too risky). He encourages Bruce’s isolationist tendencies and Bruce’s delusions, so Robin no longer leaves Gotham.  

Bruce truly and genuinely believes in the delusion that Jason never died, that the boy in the Robin suit is Jason.  He has frequent nightmares about Jason dying and starts to sleep in Jason’s room with Tim.  Tim maintains the facade that he is Jason Todd for almost every hour of his life. 

This goes on for three years, until the Red Hood comes to Gotham. At some point the real Jason Todd realizes that Dick does not communicate with Bruce, and does not know about the third boy wearing Robin. Jason successfully recruits his big brother, and they go to Gotham to confront Batman and his imposter Robin. This confrontation happens on a rooftop not far out of Crime Alley. 

Dick is the one, in the middle of this confrontation, to scream at Batman that Red Hood is Jason, back from the dead. Batman gestures sharply at Robin going ‘No. That’s Jason’. Unfortunately at the exact same time Robin goes, “does that mean I can go home now?”

Robin, Tim Drake, immediately starts to have a panic attack (he had broken one of Alfred's main rules, which was to never even imply he was anyone other than Jason Todd in front of witnesses, particularly Bruce).This is also what punctures through Bruce’s meticulously maintained delusion and Batman descends into something that is not a panic attack, but is some sort of visible crisis that includes him looking wildly between the now unhelmeted Red Hood with Jason’s face and the panicking Robin, whom he had thought was Jason Todd. 

Dick and Jason realize that, whatever is going on, they do not have all the information they need. Luckily Jason did have a safehouse nearby, which they managed to usher the still visibly in distress vigilantes into and into separate rooms to try and figure out what is happening. 

Dick goes to talk to Bruce, on the grounds that Jason is still having some Lazarus issues and Bruce may be having some Jason issues. Jason goes to talk to the little imposter Robin.

Jason does manage to get the boy in the Robin suit calmed down from his panic attack and, though he does not get all the information he does learn the following: the teen thankfully knows that he (the teen) is not Jason, the teen does not want to be Robin (and had, in fact, been abducted), and heartbreakingly that Alfred was somehow involved. Jason asked the kid’s name and was eventually told that it is Tim Drake (Jason has not heard enough news in the past few years to know who that was). Jason calls Tim by name and Tim burst into tears, as this was the first time he had been called by his real name in almost three years, and was crying so hard that Jason eventually had to sedate him (I just want you all to know that, as I was thinking of this scene I got a strong vision of Tim bursting into tears, Jason panicking and hitting Tim with a judo chop al la Austin Powers-complete with saying ‘Judo Chop’- but eventually decided to go with sedatives instead). 

Back with Dick, he also ends up having to sedate Bruce eventually (who is in the middle of some kind of break with reality). Bruce goes on an unhinged rant that, among other things, had Bruce accusing Dick of abducting Jason three years before and replacing him with the child currently in the Robin suit, accusing Dick of working with clayface to create a fake Jason (The Red Hood) so Dick could abduct the Jason currently in the Robin suit, accusing both Jason’s of not really existing (he did this a couple of times, at one point insisting that Jason-either or both of them- was really the spirit of all the kids that died in Gotham, there to torment Bruce for his failures). It becomes clear to Dick that Bruce does not remember that Jason died, that up until their confrontation Bruce truly believed that the teen in the Robin suit was Jason Todd, and that there is something very broken with Bruce. 

Dick and Jason reconvene. Once Jason says the name the teen gave, Dick has to sit down for a bit. Because the kid in the Robin suit believing himself to be Tim Drake (Whose reported death about three days after Jason’s was national news) means one of two things is likely true. One, The stress of being forced to play one dead boy has caused this child to think he is a different dead boy. Two, Tim Drake never died and has, in fact, been held captive in Wayne Manor and forced to play being Jason Todd for the last three years. 

Neither of these things are good options for either Tim’s (Jason is sure that Tim is the boy's actual name, based on his reaction) long term mental health. 

Now Dick and Jason have to figure out who, exactly, they are going to contact about this. It has to be someone within the hero community, someone who either already knows or reasonably could be told Batman’s identity.  Alfred is entirely, regretfully not a  possibility (for rather obvious reasons). Wonder Woman and Superman are also not possibilities (they are Batman’s best friends and they did not realize that Bruce was broken-and frankly, that there was a different child in the Robin suit, who may have been there against his will). Jason doesn’t know anyone  in the Hero community any longer.  The Titans that Dick has been working with look to Dick for for guidance and are not the ones he can go to for this. However, thinking of the Titan’s made Dick think of Wally West (best friend and recent boyfriend) and with him came The Flash, Barry Allan, and his family.  Barry, who knows Bruce’s identity but had been strictly professional with Bruce since the fight Alfred had instigated with Dick (so had no cause to realize that something was wrong with Batman). Barry, whom Dick had been going to with all the things he could no longer go to Bruce for. 

Dick goes to call Barry about the shitshow their lives just became. Jason goes to take off as much of the costume from both the unconscious vigilantes as he can. Incidentally he has the supplies to scrub off the makeup Tim is wearing to make himself look like Jason Todd.  

Once Barry arrives he can confirm that Tim is actually Tim Drake (There was a lot of aging and deaging the photo they had of Tim to try and either prove or disprove the corpse was actually Tim which he had a look at, as Alfred had the bodies buried in Central City-to further confuse things by crossing jurisdictions). The one thing that any of them is sure of is that Tim Drake would need lots of therapy.  

Barry, Jason, and Dick start to make plans for what to do, while they wait for the sedatives to wear off. There is no way for this to be quiet, everyone is going to be hard pressed to keep the Bruce Wayne is Batman secret under wraps. Returning Tim to his parents, if that is what he wants, will be national news.  When it becomes known that his abductor was tied to the Waynes, depending how complicit Alfred and Bruce are, then there is no way to keep this from becoming international. 

This is one where I don’t think that Tim would want to have anything to do with Batman, Robin, any heroes, or Gotham ever again. Nor do I think he would feel comfortable with anyone altering his memory. He is quick to assure Barry that he(Tim) will not tell anyone the identities that he knows if he is allowed to leave.  The only thing that Barry insists on is that Tim choose from a list of Justice League approved Therapists (So that Tim can talk about any part of the last three years, no need for hiding his identity).

After Barry asks some careful questions of both Bruce and Tim, they manage to piece together enough of what happened and get the rest of the league involved.  Both Alfred and Bruce are taken into custody, for different reasons. Bruce wakes up still in the middle of a break from reality and is a danger to himself and others. Alfred is taken into custody for the crimes he committed in turning Tim Drake into Jason Todd.  After an evaluation by Dinah it is determined that a comfortable set of rooms would be designed at Superman’s Fortress of Solitude for Bruce, while they try to heal his broken mind. Alfred would be imprisoned with Bruce as his caretaker (The only person that Alfred would not be a danger to is Bruce, and Alfred could clearly see that his actions in maintaining the delusion that Jason never died has done harm to Bruce). Should Bruce get well again, he would be released (as he had committed no crime), but Alfred would serve the rest of his life incarcerated somewhere.  

The official story was that after the presumed death of his son, Jason Wayne (with the added spice of Jason being Bruce’s biological child-to clear up inheritance),  Bruce Wayne fell into a deep depression.  In a well meaning but deeply disturbing attempt to bring Bruce back from the depths he had sunk to, the family butler, Alfred Pennyworth, had successfully abducted a neighborhood boy, killing his nanny and another child in the process to throw off the trail, who looked similar to Jason Todd.  Alfred proceeded to turn the boy into a replacement Jason Wayne, while gaslighting Bruce into believing that he never found Jason’s dead body, that Jason Wayne was still alive. As it turned out Jason Wayne had not been dead, just abducted himself for human trafficking purposes.  When Dick, a lower level agent with the FBI and estranged from his family in Gotham, helped raid one of the facilities he found his presumed dead brother. He brought Jason home, only to find that there was another teen being called Jason Wayne.  Upon finding out what Alfred had done Bruce Wayne regretfully contacted the proper authorities and was checking himself into a place where he could get real help, which he clearly needed, he left WE and all of his assets in the care of his newly returned son Jason.  Jason, like his father before him, largely left running the company to Lucius Fox, and later his daughter Tam Fox.

Not far from the truth, just lacking in the superhero elements. 

Tim’s parents were overjoyed to find that their son lived. His own presumed death had opened their eyes to some things. They want him travelling with them, which Tim was ecstatic about. The Drakes agreed that Bruce was almost as much a victim of Alfred Pennyworth as Tim himself, and agreed not to press charges against the Waynes on the conditions that the Waynes not try and contact Tim, ever. To which they agreed readily. In another life he could have been their brother, in this one they represented his torment. 

Tim never goes back to Gotham and, after his therapy is done, does not seek out vigilantes or heroes. He travels with his parents until he was in his late twenties (both he and his parents were a little clingy after the trauma of what he went through),  before he is finally ready to fly the coop, right into sailing around the world. During this sailing trip he met Bernard Dowd, another former Gothamite. They fall in love and have a wedding in a Greek temple (Bernard's Parents refuse to attend due to rampant bigotry, The Drake parents sneer at the Dowds-because there will always be part of the Drake parents that remember coming home to a missing/dead child with all the horror that implies and then the double edged sword of Tim being alive but with the trauma he had to endure- and convince Bernard that he should take Tim’s last name, that Jack and Janet were his parents now). 

In the quiet abyss of slumber

Stolen away from an empty home

Only to wake to familiar world

Not yours

Not quite

But close enough

You've been here before

Not as yourself 

But as a traveler seeking their twin

Searching for their other half

They shouldn't know you

In fact 

They shouldn't be alive

They should be codes and pixels

A world just imaginary 

Just fantastical and nothing more

Yet here you were

In a bedroom not your own

Surrounded by people you've seen

You've played with 

But by all means shouldn't be

You did not belong 

No matter what they claim

And yet here you are

The world will change 

Just as you already have

After all

Are you sure you've seen these people before?

Are you sure you do not belong here?

Do you remember your past?

Of your empty home filled with memories?

Memories you can't remember?

You don't recognize their names

And certainly not their faces

So how are you so sure you've met them before?

How are you sure you've been taken?

You're here aren't you?

They all seem so worried

And they know you so well

Hm?

Oh dear

Maybe you've been dreaming too long

You're starting to get everything mixed up

Don't worry

They'll take care of everything

And they'll take care of you

You shouldn't worry so much

I'm sure it's a little confusing

And I can sense your panic from here

Everything will be just fine

Besides

This life isn't so bad

I'm sure you'll grow to like it

It's all that you have now after all

The shatter of mirror fractals

Like the chiming of bells 

A fog settles and sinks

Muddling memory and thought alike

A drop in an ocean 

The ripples become waves 

And the waves rise into tsunamis 

As one life ends 

Another begins 

Stolen from a mundane world

To be exalted above all 

And chained to a throne

Meant for a righteous God

Is this a blessing?

Or perhaps it is a curse

Either way

It's far too late 

The die has cast 

And it's already begun 

No time for regrets

Not that you would remember any

Let's make the best of this