The Hive Alive Timeline · 10:55pm Dec 31st, 2016
A convenience for the reader. For those who wish to refresh themselves, jump in the middle, or read Hive Alive in about 15 minutes. 
PART 1 OF 5
Part 1: Chapters 1-10
Part 2: Chapters 11-20
Part 3: Chapters 21-30
Part 4: Chapters 31-40
Part 5: Chapters 41-50
Below is a spoilered super-short summary of the entire story that will only take a minute to read. However, due to the shortness, many details are left out (over 230,000 words of details). I recommend reading through all of the chapter summaries in the timeline or reading through Hive Alive itself if you have not done so previously.
Princess Twilight Sparkle lives with Chrysalis in ponyville and gets a hivemind. She also obtains guards and maids. The Mane6 become integrated into the hivemind along with some of her servants. Romantic relations develop between Twilight, Chrysalis, Fluttershy, and Rainbow Dash. Twilight and her hive members gain additional Hive Powers on top of their power of the Elements.
Sombra is believed to be alive and the royal sisters leave Equestria for a journey along with Discord after announcing Twilight as Queen of Equestria. Cadance and Shining armor also leave on a separate journey, leaving Spike and Rarity to watch over the Crystal Empire. A coup takes place to dethrone Twilight but fails. In the end, a cloud poison causes Cloudsdale to plummet to the ground.
Twilight comes home late after the crowning ceremony in which she is declared the new alicorn princess of Equestria. Four Royal Guards are detailed to Twilight. Centurion, Direway, Midnight Strike, and Flash Sentry. Chrysalis, now living with Twilight at the Golden Oaks Library after the events of Queen No More, renovates the pony’s bedroom into a dark hive chamber with a special but mysterious green-lit “sleeping ring.” Spike enjoys the upgraded sleeping arrangement. Chrysalis also mentions a few details of changelings.
Chrysalis makes the suggestion to visit Fluttershy at her cottage. Twilight does not yet know the reason why but wanted to see her friends anyways and thus goes along with it. Fluttershy reveals how useless she feels in comparison to their other friends and saddens over her lack of flying ability, which even Twilight can now practice at.
Chrysalis begins creating a special sleeping ring for Fluttershy’s bedroom and informs the others it’s only a nice gesture (giving the assumption there is no hidden motive). Twilight and Fluttershy have a private walk together where the alicorn cheers her up and tells her she will be there for her. Meanwhile, the changeling is suffering from the lack of a hivemind and wants to connect Twilight, herself, and her friends with it in order to relieve the pain. She finishes the secret hivemind connection for the ring just before Twilight and Fluttershy return.
Chrysalis suggests visiting Pinkie Pie next but Twilight gets suspicious. Chrysalis needs to connect the guards so the royal sisters don't find out. Twilight orders Chrysalis back to the Golden Oaks Library to have a talk about the rings and what seems to be on the changeling’s mind.
The pony sensed that Chrysalis had been using large amounts of magic and even siphoning some from her. Chrysalis admits being low on energy and feeds from Twilight’s close friendship while also using her own tricks to put the pony to sleep. With Twilight out of it, she goes to the guard cottage and sneaks in a hidden ring transmitter to pull one of the guards into the hivemind as well.
Twilight awakes from a nightmare and Chrysalis is there in time to comfort her. The changeling tells of a story of her people named As a Star. The alicorn suspects Chrysalis did something while she was sleeping and takes off for Pinkie Pie after asking some questions to the guards on duty.
Twilight finds that Chrysalis had not been to Pinkie’s. The pink pony drags Twilight on a crazy-filled trip to Rainbow’s. The blue pegasus greets them proudly and takes Twilight for some wing training. Something is different about Rainbow, however. She seems even happier than expected.
Chrysalis knows that Twilight has to be the one to take the lead with the formation of the hivemind or it will fail. Spike’s questioning of the changeling gets dodged. Rainbow’s training of Twilight finally ends and the purple pony begins to think Rainbow is hiding a soft side.
Owlowiscious returns from an errand Twilight gave him. He gives her a special black crystal that has some dark mist emanating from it. The alicorn princess knows the crystal is like the ones from their encounter with King Sombra. Chrysalis succeeds in keeping her true plan hidden from Twilight but fails to do so regarding the crystal.
Chrysalis explains the crystal came from a colt she knew many years ago from her grandmother. She expresses that she could defeat Sombra herself if on a full stomach. Twilight breaks down from stress and is recovered by those living with her.
The changeling tells her own knowledge of Sombra. He was originally an Earth pony prince from some kingdom beyond the eastern desert. His horn is made from dark magic. Before that, however, he had come to the changelings, seeking a pony from a vision he had. The prophecy was of a princess of great power, him marrying her, and then ruling an empire of immeasurable prosperity.
When he gave up on finding the princess, he built the empire instead, expecting her to come to him. That empire became known as the Crystal Empire, after the unique skills of the ponies within and Sombra’s use of the crystals as magical amplifiers. His horn was a magical creation of the arachnes of the far West.
Chrysalis herds Twilight to bed.
Further introduction of guard ponies. Four pegasi guards were assigned to Twilight so as to be capable of following the princess in flight.
Centurion: senior veteran guard with pastel red coat / gold mane.
Midnight Strike: second-command veteran ex-Luna guard with dark blue coat / silver mane.
Direway: special forces guard with dark gray coat / near-black purple mane.
Flash Sentry: junior guard with orange coat / blue mane.
Chrysalis helps put Twilight to sleep in the library sleeping ring and begins the first hivemind connection. The first connection is with Midnight Strike, who is upset over the termination of his watch over Luna. Twilight helps cheer him up and accept change. She takes control away from Chrysalis and makes a direct connection with him. They are mentally linked, having seen each other’s lives in a flash.
Fluttershy enters the hivemind.
Twilight is peaceful in addressing Chrysalis in the hivemind, taking a calmness and understanding from Midnight Strike that she hadn’t had before. She then connects with Fluttershy and sees the mare’s troubles and past that had been hidden away before. The beginning of romantic feelings with Fluttershy are furthered here from the earlier talk at the cottage.
Twilight better understands what it means to be a changeling queen. She accepts Chrysalis’ offer of the hivemind. Spike was absent from that night’s hivemind in spite of being in the ring. The next morning, Twilight is writing furiously about her new knowledge and then takes off swiftly for Fluttershy’s cottage. Spike and Chrysalis, still at the library, have a chat over what the changeling knows about dragons.
Princess Celestia receives Twilight’s letter about King Sombra still being at large. Twilight, now at Flutershy’s cottage, comforts her over the resurfaced memories of foalhood. Her single parent had abused and abandoned her, but she kept much of her past as a secret even from Rainbow Dash.
Fluttershy accepts having Twilight be somepony special to her. Twilight promises to be the pony in her life that will care and love her in whatever way she needs.
Rainbow Dash worries over a secret of hers getting out. That she likes kids and might want to have one someday.
Twilight considers going out of town with Fluttershy and her guard, Midnight Strike, to do some investigating on Sombra. The alicorn concludes she has limits with adjusting to the hivemind and thus only has Midnight Strike in her confidence rather than all of the guards. She makes him give his word to follow her in complete loyalty as a queen’s guard. She also orders Chrysalis to remain at the library and not go out. Twilight, Fluttershy, and Midnight Strike head out to the Crystal Empire with the intention of being back within 30 hours.
Chrysalis decides to use her time studying the black crystal. She successfully morphs it but does not have full control over the dark magic. She realizes Sombra could have used light spectrum magic and Twilight was likely off hunting for him with that in mind. Chrysalis worries for her safety and takes off after her.
When is more of the timeline coming? And I'm sad that I didn't know of the sequel till now. I have to re-read all of the series now XD.
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You may have seen the answer I've given elsewhere but It would be useful for others to see here as well if they read this. As updated above, I currently plan to get the rest of the Timeline out by the end of June this year. So by the end of next month if my work plans don't change.
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Awesome ^_^.