(I decided to include some anon’s fan theory that was later jossed rather hard. But’s interesting enough to read so here it is.)
 
Here, OP (and others). Allow me to give you a decent direction for this flashback, and the excuse to put Emerald in the ball ring/ejaculation-prevention device:
 
The guard leaves Emerald and Papillon alone; he does this after a bit of coercing from the filly and is finally convinced when Emerald also plays the snobbish royal and insists that if they’re afraid of what Papillon’s parents from another castle could do to them, just imagine the wrath of his own parents for disobeying the young Master. They wouldn’t want to cause an inter-noble incident because they offended the play date of Emerald or ruined his time.
 
The guard scrambles away, and keeps the other guard out as well. Papillon is a bit taken back by Emerald’s hint of snob-posh, and finds herself giving a little wink from more than just the book. Emerald climbs over her, telling her to read along with him; of course the little filly tries her hardest to keep up her charade. He whispers to her, pretending to read over her shoulder as he mounts, abut how the pirate takes the princess as his. Eventually the reading stops as he slides in; Papillon attempting to mutter condescending things as Emerald’s hooves mess up her gown. Emerald whimpers at the feeling, Papillon’s tightness as surprising as her literal and metaphorical shallowness.
 
The filly’s chiding dissolves into muffled squeals of delight; the young Emerald begins a feverish humping that only an inexperienced yet promising colt can provide. After Papillon climaxes for perhaps one of their first times via penetration, he flips his girly mane and asks if she’s enjoying the story. She merely grunts, her young mind unable to formulate a reply as her fillyhood squeezes involuntarily.
 
Emerald bites his lower lip, his colthood swelling with need. Small tears form as his rear knees shiver and buckle every other thrust into his spoiled, bitchy lover. He squeaks her name with a crack, unable to fight the overwhelming sensation thundering though his body. He tells her in a wobbly voice that she’ll love the ending, that she should read it aloud to them since she’s so talented. Something in Papillon’s brain tells her to yell at Emerald for pawing so roughly atop her dress, but a far louder voice inside begs for something far more important from the colt, something only her id can place; grunting his name, dipping her head to read the final sentence with a shout…
 
>“H-he makes her pregnant!”
 
Emerald’s eyes snap open, hips thrusting once… twice, before his flaring stalk forces him still. He looks down at the little noble, buried to the hilt and poised to promise her that insistent conclusion. His subconscious flashes back to the name calling, disrespect, and arguments. The shared games, the rare laughs, the sideways glares…
 
But only one word lingers at the forefront of his psyche:
 
P-pregnant…
 
The first rope spurts thick, long, and fierce. Emerald whines loudly, laying atop Papillon’s back as he begins to empty his load. His testicles, certainly impressive for a colt his age, contract almost painfully at the thought of flooding Papillon’s womb. Five, six, seven… he loses count as the gravity of his lust’s commitment sinks in. His hips shudder, only serving to brush his sperm-heavy testes against the filly’s winking nub, triggering another climax that wet their thighs.
 
He shouldn’t be doing this. He shouldn’t be having a foal with somepony so distasteful. He should have pulled out and sprayed her dress with lines of cum, her mane with dollops of cream… but none of it matters now. Only one word was emblazoned into his mind.
 
That marvelous, horrible, wonderful word…
 
 
Emerald pulls out slowly, only then noticing the small salty streaks near his eyes which he quickly wipes away. Papillon remains low, still recovering from the situation with her wrinkled dress hiked up. The sight allows Emerald to see the fruits of their labor: rich globs of off-white spill lazily from her twitching fillyhood. Deep in his psyche, a warmth floods through his brain and down his spine. It shouldn’t feel so nice; why does it feel so damn nice?
 
“He…makes her…”
 
>“T-that’s what it says, idiot.”
 
Papillon stutters, desperately attempting to recompose herself.
 
>“It’s your boo-”
 
clang!
 
A silver platter of candies clatter to the ground; the guards finally working up the courage to come back in under the pretext of delivering the sweets and hearing loud noises from the young Master and Lady.
 
The two foals scramble to hide the scene, but the damage is done. Emerald’s sperm and Papillon’s filly juice stains the once pristine library carpet, and the room reeks of sex. The guards separate the two; Papillon doesn’t understand the guards sudden assertiveness and complains to her father. The guards already know all too well the current trouble they’ll be in, however.
 
Once Emerald’s step-parents are informed of his little per-marital tryst with Papillon, their rage cannot be contained. His step-father is furious at the possibility of a child out of wedlock, since Emerald is a tool for political marriage into a possibly stronger noble family. Not only that, but the thought of his guards allowing the impregnation of a filly of another family under their supervision in his castle would cause such an uproar for justice that he couldn’t possibly hide such a scandal… not to mention the bastard child besmirching his reign.
 
Emerald’s step-mother however is furious for slightly different reasons: he came inside a different mare than her. Possibly, she seeks to sire a legitimate heir with Emerald himself at the expense of her husband. Possibly, she wants Emerald to be her own cum-filled plaything under the guise of a show marriage with Papillon, and takes the insemination of the little noble personally. Possibly she’s just a sadist, and likes to milk her step-son with a strap-on and finds the idea of him topping without her permission infuriating. Possibly she might just hate sharing his sperm outside the family.
 
Regardless of the reasons, she sees that it will not happen again. Emerald is fitted with his orgasm-preventing ring. Then, escapes under the circumstances of using the elderly tutor to explain to him the birds and the bees. He uses the bee nest to distract everyone in the garden, especially his tutor, and escapes with the keys he grabbed from the guard that was too busy freaking out about his punishment to notice them being stolen while he dragged Emerald away from the cum-stuffed Papillon.
 

 
There you have it.
 
An explanation for Emeralds impregnation fetish, a back story about his conflicted relationship with the abusive Papillon, and why his parents put him in the ring.
 
This could be expanded on by us further wondering what happened to Papillon back at her own castle; has this changed her feelings toward Emerald? Is she pregnant? All of these could be very interesting paths for mid-late game investigations.
 
Interesting quest, OP. I do write for /mlp/, but figured I’d whip something up for the thread about Papillon having her way with Emerald and how it could actually work very well into the canon storyline. Keep up the diligent work.