The Destiny universe is a complicated and immense tapestry of lore and not everything has an answer. In Destiny 2 however, there are still too many loose ends. The game is filled with layers of storytelling attached to destinations, campaign missions, cut scenes, seasonal content, and miscellaneous activities. While Destiny 1 had mysteries like "who is the Exo Stranger" or "where are Oryx's sisters," Destiny 2 has a handful of its own mysteries.
When Destiny 2 Beyond Light launches, players will learn new information and possibly find some answers to a few things listed. The following is a list of unresolved storylines related to Destiny 2.
10 Elsie Bray Is Exo
During the Warmind expansion, it was revealed that Elsie Bray, Ana Bray's sister, is the Exo Stranger from Destiny 1. The Exo Stranger was a big mystery and players only met her a handful of times. However, she kind of disappeared from the Destiny storyline for a couple of years. Even though she was revealed to be Elsie Bray, nothing developed from that.
The interesting thing is that Clovis Bray, an influential scientist from the Golden Age, is the one who creates Exos. The question here is, why is Clovis Bray's daughter Elsie Bray an Exo when Ana is human? The mystery behind the origin and creation of Exos has been a topic of interest for a while. We may get more answers to this in the Beyond Light expansion, especially when the Deep Stone Crypt raid launches.
9 Shin Malphur And Dredgens
Rezyl Azzir was a Guardian from the Dark Age whose curiosity led him to the Moon. Azzir met Xyor, The Blessed who told him that he was destined to fall into the dark. Rezyl then defeated Xyor’s consort and used his chitin to cover his hand cannon known as the Rose, which later became Thorn. He then slowly started admiring the ways of the Darkness and became Dredgen Yor.
Shin Malphur killed Yor and created the Shadows of Yor group to trap and kill Guardians who align with Yor’s corrupt beliefs. During the Malfeasance mission, players learn that Dredgen Cull gets burned to death by Malphur's Golden Gun. The odd thing is that players get the Dredgen Seals by doing objectives in Gambit. So, where is Shin Malphur when Guardians are becoming Dredgen?
8 The Lighthouse
Oddly, Brother Vance started hearing the Lighthouses sing after Guardians died. In Chapter 4 - Revelations, the origin of Trials was revealed. The Trials were a way to research the sounds made by the Lighthouses by having a crucible-like activity where Guardians would have to kill each other.
The Lighthouses have a tone for a Guardian's death, but another tone for the Guardian's final death. Presumably, the Vex either use the Lighthouses to celebrate the death of Guardians or to communicate with something. During the Season of Arrivals, the Lighthouses have a bright beam going to the sky after the Pyramid ships arrived on Mercury.
7 Uldren Sov Returns
In Forsaken, Uldren killed Cayde-6 and that lead him to his death at the hands of the Guardian. Later, a cutscene shows a Ghost named Pulled Pork searching for someone in the Dreaming City. He found Uldren's body and brought him back to life as Guardian.
A lore entry from Amnestia-S2 hints at Uldren's new Guardian life. The lore entry describes Uldren as being lonely since other Guardians show him hostility or they have grief in their eyes when they see him. He doesn't know why since he can't remember his life before he became a Guardian. Other Guardians are aware of Uldren's revival but there's no mention of him anywhere in the game.
6 SIVA On Nessus
The Exodus Black was a Golden Age colony ship that crash-landed on Nessus due to Vex activity. The SIVA.MEM lore entry from Destiny 1 claimed that SIVA was on the Exodus Black when humanity was heading to Nessus. SIVA was used to build civilizations and it became a crucial part of the Golden Age, but later became a huge threat.
Failsafe even mentions that SIVA is in an encrypted area of the Exodus Black ship. The Outbreak Perfected SIVA weapon was re-released with the Zero Hour mission too. In the mission, Fallen are trying to get their hands on the weapon, and possibly SIVA. Brief mentions of SIVA have not yet lead to anything that announces SIVA's return.
5 Mithrax Is Friendly
In the Enemy of my Enemy quest on Titan, Mithrax speaks to the Guardian in his language and lets the Guardian complete their mission. He shows up once again during the Zero Hour mission. He prepares us to face the Fallen and Siriks, Loyal to Eramis to ensure that they don’t get their hands on Outbreak Perfected or anything SIVA related.
Mithrax has helped Guardians multiple times, but very little is known about who he really is. In the Queenbreaker lore, Mithrax says he is open-minded and wants to fight for the Traveler alongside Guardians. Also, the connection between Sirik and Mithrax may have to do with Eramis, the antagonist in Beyond Light.
4 Variks And The Prison of Elders
Players traveled to the Prison of Elders with Cayde-6 to contain the chaos with the Scorn prison break. Besides the first mission in Forsaken and the Warden of Nothing strike, the Prison of Elders is forgotten. Variks, the Loyal’s whereabouts are undisclosed even though his unattentiveness in the Prison led to Cayde-6’s death. The High Servitor was the Warden of the Prison but began to malfunction and take the side of the Prisoners.
The lore entry called Unknown Space describes Variks having a dream about the Nine right before Petra and Cayde arrived at the Prison of Elders. Variks didn't help Petra or Cayde. Varik’s whereabouts and possible new intentions as well as the condition of the Prison make for an intriguing puzzle.
3 Nokris Returns
Nokris, the other son of Oryx, was defeated in the Strange Terrain strike by a fireteam, but he isn't completely gone. In the lore piece called False Idols, it was confirmed that Nokris is still alive in the Ascendant plane and has teamed up with Savathun.
Nokris uses cunning ways to escape Mars and Savathun took notice of his efforts. She brought him into her court to get him on her side, but her true intentions are unknown. In the Interference mission, Nokris speaks a few lines when the Guardian enters Savathun's court. It was assumed that Nokris and Xol were dead after they were defeated in strikes during the Warmind expansion. However, they are suddenly brought back to the Destiny lore after 2 years.
2 Mara Sov
Guardians visited her Mara Sov every 3 weeks to gain rewards and a piece of lore. During those visits, she hinted at her plan and her intelligent connections. She seems to be close with the Nine and the Exo Stranger too. On her table, there was an image of Pyramid ships on their way and she even knew about Uldren’s revival.
On the final visit, Mara talks about a friend who says “A side should always be taken, even if it’s the wrong side.” That's the Exo Stranger's line from Destiny 1. Mara then disappears in a way similar to the Exo Stranger which could hint at the use of Stasis. How does she get her information? Her connection with the Nine? Does she have dark powers? Where is she now?
1 Dreaming City Curse
The Ahamkara Riven baited Guardians into killing her so she could unleash a last wish. This wish put the Dreaming City under a 3-week loop created by Quria where darkness grows, then vanishes and grows again. It's unclear as to why their wish was granted.
The Taken presence increased, and the line between reality and the Ascendant realm thinned. It's speculated that Savathun’s daughter, Dul Incaru, uses Mara Sov’s throne world in order to access the Distributary and to gain power from the reoccurring violence. It's still unknown why the Dreaming City and the Distributary are such big targets. Also, the curse has been repeating for a long time, but when will it stop?