Warning: SPOILERS for Star Trek: Discovery season 3 finale - "That Hope Is You, Part 2"

Star Trek: Discovery's season 3 finale wrapped up the major storylines of Captain Michael Burnham's (Sonequa Martin-Green) first adventures in the 32nd century, but many questions remain for season 4 to address. By the end of "That Hope Is You, Part 2," Michael and the bridge crew saved the U.S.S. Discovery and the United Federation of Planets from the Emerald Chain and their leader, Osyraa (Janet Kidder). Discovery also rescued their friends trapped in the Verubin Nebula and uncovered the origin of The Burn. Burnham was rewarded for her heroics by being named the new Captain of Discovery.

The Burn was the central mystery of Star Trek: Discovery season 3 and it was revealed that it was inadvertently caused by Su'Kal (Bill Irwin), a young Kelpien who was born in the radioactive Verubin Nebula and was genetically infused with dilithium. It was a strange and disappointing explanation for The Burn, but thankfully, Discovery's other adventures in the year 3189 were more thrilling. Star Trek: Discovery season 3 reintroduced the Federation as a shell of its former self, an isolationist United Earth, and classic aliens like the Vulcans and Romulans, who now share Ni'Var, the planet formerly known as Vulcan. There was an unexpected but welcome return to the Mirror Universe that led to the departure of Emperor Philippa Georgiou (Michelle Yeoh), who will soon star in her own Star Trek spinoff. Osyraa and the Emerald Chain also emerged as worthy foes for Burnham and Discovery.

Related: Star Trek: Discovery Season 3 Ending Explained

The final moments of "That Hope Is You, Part 2" gave Star Trek: Discovery a new paradigm going into season 4. Burnham's victory not only got her a long-awaited promotion and command of the U.S.S. Discovery, but it also launched a resurgence of the Federation. Meanwhile, some characters' futures are now pointed in new directions while larger mysteries remain, such as the revelation of the Temporal Wars of the 30th century and their far-reaching ramifications. Star Trek: Discovery season 3 also cemented the series as the flagship of the Star Trek franchise on CBS All-Access by honoring and integrating the legacy of the prior Star Trek series and even the alternate Kelvin timeline of J.J. Abrams' Star Trek movies. With Captain Burnham now flying Discovery into the new final frontier, here are the biggest questions Star Trek: Discovery season 3 left behind.

10. What Will Saru Do Next?

Su'Kal and Saru

In order for Burnham to assume the Captain's chair, Star Trek: Discovery season 3 wrote out Captain Saru (Doug Jones), who voluntarily surrendered command after meeting Su'Kal. Saru's new direction was seeded late in the season when he learned it was a Kelpien ship that was trapped in the Verubin Nebula, which triggered his hidden but overwhelming desire to reconnect with his people. Saru has now opted to take a leave of absence to guide Su'Kal's integration into Kelpien society on Kaminar as well as enjoy his own homecoming.

Saru finally becoming Captain of Discovery was a highlight of season 3, so it's disappointing that the starship's game of musical captain's chair continued. What surrendering his command ultimately means for Saru remains to be seen. Will he return to Starfleet? Will he become Discovery's Captain once again? Will he become an Admiral, or will he become an Ambassador to Kaminar? Saru is definitely returning in Star Trek: Discovery season 4 but it's unclear what his next steps will be.

9. Is The Emerald Chain Really Gone?

Oded Fehr as Vance and Janet Kidder as Osyraa in Star Trek Discovery

Osyraa's bold plan to unite the Emerald Chain with the Federation had merit, but the Orion Minister reverted to super-villainy when she realized she wouldn't be allowed to control the new entity she dreamed up. Ultimately, Burnham killed Osyraa and destroyed her flagship, the Viridian. The final moments of "That Hope Is You, Part 2" briefly noted that "the Emerald Chain fractured without Osyraa." Does that mean the Chain is completely defeated or will someone else take the reigns? It seems both unlikely and far too convenient that the vast and militarily powerful Emerald Chain is no longer a factor and they were excellent villains. Will a different incarnation of the Emerald Chain emerge under a new leader in Star Trek: Discovery season 4?

Related: Star Trek: Discovery's Villain Plan Explained (& Why It Should Have Worked)

8. Who Is The Federation President?

Burnham and Saru meet the 32nd century Federation in Star Trek Discovery

Osyraa expected to parlay with the Federation President but instead, Admiral Charles Vance (Oded Fehr) conducted negotiations. This left the open question of who the Federation President is in the 32nd century. Starfleet and the Federation share their hidden starbase headquarters so presumably, the President does live and work somewhere in that vast complex.

Will Star Trek: Discovery season 4 reveal who, exactly, oversees the Federation? Some fans speculate that Kovich (David Cronenberg) is secretly the Federation President while others conjecture that Lt. Adiya Sahil (Adil Hussain) will end up with the job. Will Star Trek: Discovery season 4 bear out one of those two theories, introduce a new character, or will Admiral Vance get the job as Federation President?

7. Will The Sphere Data Become Zora?

Star Trek Discovery DOT-23

The Sphere Data gained sentience in Star Trek: Discovery season 3, taking a huge step forward towards becoming Zora (Annabelle Wallis), Discovery's artificially intelligent computer introduced in the Short Trek "Calypso". The Sphere Data infused with Discovery's computer but uploaded itself into the DOT-23 repair droids when the Emerald Chain captured the starship. The Sphere Data/DOT-23s then fought side-by-side with Discovery's bridge crew against the Emerald Chain and it even sacrificed itself to save Lt. Joann Owosokun (Oyin Oladejo). By the end of "That Hope His You, Part 2," Owo and Commander Jett Reno (Tig Notaro) were able to resurrect the Sphere Data.

The idea behind the Sphere Data is that Discovery is gradually becoming sentient and that the starship itself protects and cares for its crew. Will that evolution continue in Star Trek: Discovery season 4, and will the Sphere Data take on the persona of Zora? Further, will "Calypso" actually happen, or is the Short Trek now set in an alternate future considering the upgrades and changes to the Discovery-A that aren't reflected in "Calypso"?

Related: Discovery Has A Controversial Star Trek DS9 Technology

6. Will Stamets Forgive Burnham?

Culber Stamets Adira

To keep Discovery's spore displacement hub drive safe from Osyraa, Burnham made the difficult but correct choice to eject Lt. Commander Paul Stamets (Anthony Rapp) from the starship, despite his pleas to let him jump the ship back to the Verubin Nebula to rescue his family, Dr. Hugh Culber (Wilson Cruz) and Adira (Blu del Barrio). Stamets was further humiliated when Admiral Vance agreed with Burnham and also forbade Stamets from performing his rescue mission.

Ultimately, Michael saved the day and her friends, but Stamets didn't forgive her by the end of "That Hope Is You, Part 2." In fact, Paul was the lone, unhappy holdout when Michael became Captain Burnham. Will Stamets forgive what he felt was Michael's betrayal and what will his future aboard Discovery be now that he's no longer the sole navigator of the spore drive?

5. How Will Gray Be "Seen"?

Gray and Adira

Gray (Ian Alexander) is technically deceased and his consciousness is part of the Tal symbiont inside Adira, but somehow they were able to see Gray, who was tormented by no one else being able to see him. However, thanks to the Kelpien ship's holodeck somehow recognizing Gray and creating a holographic version of the Trill, Culber and Saru were able to see Gray for the first time.

Culber promised to find a way for Gray to be seen permanently, but what will that entail in Star Trek: Discovery season 4? Will Gray be a permanent hologram or can his consciousness somehow be placed in a synthetic body like Jean-Luc Picard (Patrick Stewart) was in Star Trek: Picard season 1? It will be fascinating to see how Gray's dilemma is resolved and to see how both Gray and Adira, the first transgender and non-binary characters in the franchise's history, will play bigger roles in Star Trek: Discovery season 4.

Related: Star Trek: Every Major Character Who Died (& Was Better For It)

4. Where Are The Klingons And The Borg?

Star Trek: Discovery season 3 updated fans on the 32nd-century state of the Vulcans, Romulans, Orions, Andorians, and even Bajorans and Cardassians made cameo appearances. But notably absent were the Klingons, who were not mentioned at all. The Klingons were major (and divisive) factors in the first two seasons of Star Trek: Discovery, but fans have had no indication of what became of the warrior race (and what they look like) 930 years later. So many questions surround the Klingons, like what happened to them after The Burn happened, and whether they are still allies of the Federation or became isolationists like United Earth and NiVar.

Meanwhile, the Borg were a big part of Star Trek: Picard and the cybernetic race may remain a purview of that series, but it would still be fascinating to learn what has become of them in the 32nd century. Have the Borg finally been defeated, or have they evolved to no longer be a menace? Did The Burn also affect the Borg? Star Trek: Discovery season 4 needs to provide some answers and hopefully even face one or both of these popular species.

3. Will Tilly Get A Command-Level Promotion?

First Officer Tilly

The ending of "That Hope Is You, Part 2" indicates that Ensign Sylvia Tilly (Mary Wiseman) will remain as Captain Burnham's Acting First Officer, but she is due for a command-level promotion to Lieutenant if she's going to remain in that role. Although Osyraa's hostile takeover of Discovery exposed the limits of Tilly's command experience, she still conducted herself heroically as Number One. Tilly is a long ways away from being ready for the Captain's chair, but she also can't continue to be the lowest-ranked member of the bridge crew while doubling as First Officer.

2. If Book Is Staying On Discovery, What Happens To His Ship?

Book Spore Drive

Michael's love affair with Cleveland Booker (David Ajala) was one of the best aspects of Star Trek: Discovery season 3 and the empathic Book found a new purpose aboard Burnham's starship as another navigator for the spore drive. This keeps the couple together, although a civilian like Book being romantically involved with a Federation starship Captain is bound to create issues in Star Trek: Discovery season 4, not to mention how this affects Lt. Paul Stamets' role as spore drive navigator.

Related: Star Trek: The Disgusting Truth About Discovery's 32nd Century Food

However, Book (and his beloved cat Grudge) remaining aboard Discovery likely means he's retiring from his job as a courier, so what happens to Book's shape-shifting starship? Will it continue to remain parked in Discovery's shuttle bay (and take up an enormous amount of space)? Will it be commissioned as a Starfleet ship and put into other use? Book's ship came in very handy during Star Trek: Discovery season 3 but it can't just live aboard Michael's ship permanently, can it?

1. Will Michael Burnham Remain Captain For All Of Star Trek: Discovery Season 4?

Captain Burnham Finale

Michael Burnham owns the most colorful Starfleet career of any Star Trek character. Burnham began the series ruining her own career and becoming Starfleet's first mutineer before she fought for redemption, regained her rank as Commander, and then she "saved all the things" on the first two seasons of Star Trek: Discovery. Michael began Star Trek: Discovery season 3 doubting she even had a future in Starfleet, only to accept Captain Saru's offer to become his First Officer and then flame out in spectacular fashion by abusing her authority to perform secret missions. But Commander Burnham still found herself on a trajectory to become a Captain and her heroics won her command of Discovery, to her surprise (and to the surprise of fans as well).

Captain Burnham is undeniably brilliant, talented, and heroic; she is now a hybrid of her adoptive brother Spock's logic and intelligence and Captain James T. Kirk's risk-taking courage to do what needs to be done regardless of consequences. Still, as deserving as Michael may be, there is no guarantee she will remain Captain of Discovery all the way through season 4, since Star Trek: Discovery still continues its practice of rotating who sits in the big chair. For all of the shocking but heroic actions that Burnham is capable of, Michael actually holding onto Star Trek: Discovery's Captain's chair in season 4 would be the biggest surprise of all.

Next: Everything We Know About Star Trek: Discovery Season 4