Spike is cleaning the library, and is almost finished, when the Cutie Mark Crusaders crash into the room and destroy all his hard work. He is annoyed, but even more so when, though the other two crusaders apologise, Scootaloo makes a snarky remark about how easy it would be to just re-clean. He physically hits her on the head (lightly, but enough to cause pain), causing her to cry and the three to run off. Spike shrugs and starts cleaning again.
A little while later, Rainbow Dash finds out and bursts into the library (again causing Spike's work to be ruined), and starts yelling at Spike. Twilight, who has returned home at this point, hears about what happens and asks Spike if it's true. Spike confirms it nonchalantly. Twilight then gets mad as well and demands that Spike go apologise, but Spike refuses, claiming that Scootaloo deserved it.
Upon hearing this, Rainbow hits Spike, and is about to ask how it feels when Spike hits her back, using his claws to draw blood. Twilight again tries to make Spike apologise, and he again refuses, stating that Rainbow also ruined his work, and hit him first (IMPORTANT: Spike says that matter-of-factly, not angrily. At no point in this story should he actually get angry). Twilight grounds Spike and sends him to their room, which he enters while looking confused. Rainbow asks what is going on, to which Twilight responds that she has no idea.
Some filler happens here, in which a rift is formed between Spike and the Mane 6. Actual content is author's choice, but through all of it, Spike should get more confused, not angry. He can get sad, though. Eventually, Twilight gets Celestia to come help her, as she's at her wit's end. She and the Mane 6 all go to the library to talk to Spike. Celestia asks Spike why he thinks hitting Scootaloo/Rainbow was acceptable.
It's at this point that the story may not be believable
Spike reveals that he honestly does not see anything wrong with what he did, as he was taught that violence is an acceptable social interaction. Citing at least one instance of abuse from each of the Mane 6 (Iron Pony competition, Rarity's pincushion, Fluttershy might be hard), it becomes clear that Spike saw all of these events as being normal pony behaviour. So, when Scootaloo messed up his work and mocked him, he responded in the way he assumed the Mane 6 would (Twilight, particularly, as she would shove him aside with her magic when she was annoyed like he was).
Celestia, as Spike's mother, is furious to learn this. After asking Spike to leave her with the Mane 6 (who are horrified at what the dragon said), she rants at all of them for hurting her son and teaching him such horrible things. In particular, she is disgusted with Twilight, whom she trusted to raise Spike. Afterwards, she goes to Spike and tells him that he'll be living with her back in Canterlot for a time. When asked when he can come back, Celestia is hesitant to say that she has no intention of letting him return, and instead avoids answering by manipulating Spike, asking if he's that eager to get away from his own Mother.
At this point, the story splits into two parts, and should alternate accordingly. The Mane 6's part is in looking at their own behaviour and their treatment of Spike (and each other, if applicable), and coming to terms with their own guilt. Rainbow Dash, in particular, has to tell Scootaloo that Spike hitting her is essentially Dash's fault, causing Scootaloo to get angry with Rainbow and stop talking to her. After some self-pity, the girls rally and resolve never to treat Spike or anypony in such a way again, and to find some way to make it up to him. They head to Canterlot with this goal in mind.
Celestia's part is in re-teaching Spike that such behaviour is not acceptable, and that he owes Scootaloo an apology (purposely leaves out Rainbow Dash, out of anger). This will be a delicate, long-term process, as to teach him this will inevitably involve Spike realising just how much the Mane 6 have abused him over the years. Celestia wants to avoid a situation where Spike turns bitter as a result of this realisation. As it is, when Spike does connect the dots, he breaks down crying, leaving Celestia to do her best in comforting him. The morning after, when Celestia must leave to perform her duties while Spike is still asleep, her first appointment for the day is the Mane 6 (Story becomes one again here).
The 6 state their case: they're sorry, they want to make it up to Spike, and they will never hurt him again. Celestia is unconvinced, so Twilight steps forward and offers her personal apology. Twilight knows that Celestia trusted her enough to raise her own son, and to protect him from the world of the nobles, who would have used him against Celestia or demanded he be sent away. She betrayed that trust. She is willing to lose her position as Celestia's student, but she begs for the chance to reconcile with Spike, claiming that she cares for him as deeply as Celestia does.
After some contemplating, Celestia reveals what happened last night, and how deeply Spike is hurting right now. She is extremely disappointed in all of them, and were it not for the fact that she was a princess and they the Elements of Harmony, she would personally annihilate them all. However, she can see the sincerity in their eyes and words, and she knows that they have the best chance of reaching Spike right now. She allows them to see Spike, and says that he may decide for himself if he forgives them and if he wishes to continue living with Twilight. However, she also warns them that this is the only chance they will receive. If they do hurt him again, then princess or not: she will end them.
The 6 enter Spike's room. He has recently woken up, and is crying lightly when they enter. There is awkward silence, until Spike asks why they did what they did. They explain (one, a few, or all of them may be part of this, author's choice) that, since he is not a pony, on some level they never thought he needed to be treated as one. They insist that they are wrong though, and they beg his forgiveness, as well as promising that they will never treat him in such a manner again (Twilight's personal promise is to never use magic on him against his will). Spike is quiet, then runs up to hug them, saying they're forgiven, and that he still wants to be friend. Ending is mushy hug scene.
A possible epilogue, if desired, should be where Spike goes to the CMC clubhouse to apologise to Scootaloo, who accepts since she understands why. For extra feels, Spike can also convince Scootaloo to give Rainbow Dash another chance, like he has with the Mane 6.
Just noticed, but a possible sequel is one in which Twilight has to work to regain Celestia's trust. She might've let Spike return, but it doesn't mean she's completely forgiven Twilight.