This is a alternate ending to The Last Crusade.

After Snap and Mane say that they’ll going away and taking Scootaloo with themselves, the little filly ran off in tears. While running, she bumped into Windy Whistles (Rainbow Dash’s mother). The tan-orange maned mare was surprised at first, until she saw the tears stream down Scootaloo’s face. Worried, Windy asked what was wrong. Scootaloo couldn’t answer straight because she was crying a bit too hard to speak properly. Now more worried, Windy wrapped her hooves around the filly and carried her to hers and Bow’s home.

When they reached the house, Bow Hothoof was also surprised and worried when he saw the state Scootaloo was in. After giving the filly some cupcakes and a glass of milk, the married couple asked her what was wrong. Scootaloo then told them everything, all about her parents going away for so long and leaving her in the care of her aunts. Whenever she wrote a letter to them, she never got a reply. Things only got worse when her aunts get killed in a train crash. Her parents finally return, but instead of staying, they decide to make Scootaloo move away with them. Scootaloo doesn’t want to leave or even be with her parents since they never even bothered being there for her to give her love or support.

Bow and Windy are both shocked when they hear all of this. The two ponies feel really sorry for the little filly who starts breaking down in tears again. Amidst her tears, Scootaloo confess that she had always look at Bow and Windy as if they were her real parents ever since she met them and wishes that they actually could be. She then looked down in sadness, thinking that they never could. However, much to her surprise, the two smile warmly and admitted that they’ve come to think of her as one of the family as they love her. Windy then walked up to Scootaloo and told her that she had a way to help the little filly forget all about her worries. You see, Twilight had casted a special spell on Windy so that she had the power to hypnotize others to help them relax. Scootaloo wasn’t so sure at first, but Windy reassured her that no harm would come. As she trusted the mare, Scootaloo looked into her eyes.

Once they had made eye contact, Windy closed her eyes and when she open them they changed into colourful rainbow spirals. Scootaloo was taken aback at first, but she say nothing and kept looking into the mare’s eyes. Soon the little filly’s own eyes mimicked the same colourful spirals in Windy’s eyes. Red, orange, yellow, green, blue, and purple on repeat. The tan-orange maned pony reassured the filly that she didn’t need to go back her so-called fair weather parents. Windy then said that Scootaloo can live with her and Bow and that they take good care of her and give her all the love and support she deserves. The little filly’s gaping mouth closed to form a grin. Now hypnotized and happy, Scootaloo said that she would love that and calls Windy “Mom”.

Pleased, the light blue pony gave the filly a hug. Bow, impressed, soon joined the hug. Scootaloo then gave a cute little yawn. Smiling warmly, her new parents carry her upstairs to her new bedroom which happens to Rainbow’s old room. After getting the hypnotized filly into some purple footsies, Bow and Windy tucked her into bed. Scootaloo then happily fell asleep, wearing the cutest smile on her face. The two ponies then each give her a goodnight kiss and then left the room.

After signing the papers, and getting approval from Snap and Mane who admit that it would have been difficult to take care their child and go on their missions, Bow and Windy bring all of Scootaloo’s things up to their home. As soon as the little orange filly wakes up and is overjoyed when she finds out that Bow Hothoof and Windy Whistles are now her official parents and guardians. Rainbow Dash is also overjoyed that she and Scootaloo are now official sisters.

Windy would still sometimes use her hypnosis to either to help Scootaloo relax or sleep. Scootaloo loves her new home and she especially loves new family.

This picture is inspired by Snakeythingy: https://derpibooru.org/tags/artist-colon-snakeythingy

Headcanon:

Scootaloo is adopted by Bow Hothoof and Windy Whistles.

The events of Season 8-9 (With the exception of The Washouts and Best Gift Ever) and Rainbow Roadtrip are not canon.

Note: If anyone wishes to do a fanfic on this, by all means, go ahead! ^^