Warning! Spoilers for the Loki series ahead.
The branching out from the Sacred Timeline. From there, the trickster was sent on a brand new adventure separate from his brother, Thor (Chris Hemsworth). He's given a chance to carve his own path as he understood the inner workings of the organization that took him into custody, meeting his variants along the way.
But, before the Loki show can jump to this uncharted territory for Marvel Studios, it needed to explain how and why the Asgardian Prince is still alive despite his clear death at the hands of Thanos (Josh Brolin) in Agent Mobius M. Mobius' (Owen Wilson) and blackmail a desk officer, Casey (Eugene Cordero), to return the Tesseract which was confiscated when he was arrested. He then realized that the powerful gems that the Mad Titan was hell-bent on collecting are treated as if they're nothing in the TVA.
This was emphasized visually when Loki opened a drawer full of colorful crystals. In the pile, there are several Reality Stones (red), Power Stones (purple), and Time Stones (green). There's one Space Stone (blue) and Soul Stone (orange), alongside other knick-knacks. Interestingly, there's no Mind Stone, although one can be seen in the credits, functioning as a paperweight as Casey claimed he and his workmates tend to do. There hasn't been a proper explanation regarding this in the Loki show, leaving fans speculating what this could possibly mean in conjunction with the bigger MCU. Here are some of the most popular theories about it.
Loki Only Showed TVA's Haul For The Day
Arguably the most practical explanation for the absence of the Mind Stone in the TVA's haul is that it only showed that day's collection. It's possible that after one round of variant arrests, these were the only Infinity Stones accumulated. Aside from the Lokis, the Loki series didn't show much of the other variants. During the God of Mischief's preliminary booking, before he faced Judge Ravonna Renslayer (Gugu Mbatha-Raw) for his case there were other variants who are being processed including a Skrull. But for the most part, the processing area was almost empty. Perhaps it was a slow day, and the hunters weren't able to encounter a variant who was in possession of the Mind Stone.
In conjunction with this theory, it's also possible that other TVA agents have already picked the Mind Stone from the pile to use as paperweights. This is backed up by the shot in the credits where it's prominently used for this exact function. Since the Infinity Stones seemingly don't have their powers in the TVA offices, not to mention the fact that the Minutemen are convinced that they are created to serve the organization, it's likely that no one would dare steal it. Given these, chances are that there's no deeper meaning as to why the Mind Stone wasn't in the pile of elemental gems that Loki saw in the TVA.
The Mind Stone Is Connected to Scarlet Witch Who's Also A Nexus Being
While Marvel Studios is ready to move on from the Infinity Saga with Loki emphasizing that the Infinity Stones have barely any significance moving forward, the Mind Stone is the only gem that still carries weight in the future of the MCU. In WandaVision, Agatha Harkness (Kathryn Hahn) claimed that it amplified Wanda's (Elizabeth Olsen) inherent powers. This was quite different from the previous assumption that subjecting the Maximoff twins using the stolen scepter from the Battle of New York was what gave them their super abilities.
At the end of WandaVision, however, Scarlet Witch eventually offered a clear explanation regarding her bond with the gem. During her final farewell with Vision (Paul Bettany), she detailed how she's able to recreate the synthezoid, saying that he's "the piece of the Mind Stone that lives in me." This means that the Mind Stone actually transferred some of its powers to her and she's able to tap into that making the recreation of Vision in Westview possible. Since Scarlet Witch is a Nexus being, the TVA might not be able to easily acquire the Mind Stone as it would mean outright coming for Wanda's powers.
Loki's TVA Is Missing The Soul Stone — Not The Mind Stone
Looking back at the scene, perhaps the assumption that the Mind Stone was missing from the TVA's drawer is wrong. Instead, it could be the Soul Stone that is not there. The selection includes a yellow-orange gem which at first glance appears to be the Soul Stone in the MCU. But, it is much bigger compared to its previous incarnations. Thanos' gauntlet had five similarly-sized placements on each knuckle; throughout Infinity War, he filled them up with the Power Stone, Space Stone, Reality Stone, Soul Stone, and Time Stone. Meanwhile, the Mind Stone, which was the last gem he acquired, was placed at the center of his hand with a noticeably bigger slot. Maybe, the bigger crystal in the TVA drawer was actually the Mind Stone, the lighting was just a bit off so it looked more orange than yellow like the Soul Stone.
This makes sense when it's taken into consideration the fact that acquiring the Soul Stone is very difficult. For starters, it's not as readily accessible as the rest of the Infinity Stones; it's guarded in Vormir. Secondly, possessing it requires a sacrifice. Thanos was so committed to his cause that he killed his favorite daughter, Gamora (Zoe Saldana) so he can collect all the Infinity Stones. Meanwhile, Black Widow (Scarlett Johansson) was so desperate to bring back those who were snuffed out of existence by the Mad Titan's snap that she was willing to die for the Soul Stone.
Loki season 2 will return on Disney+.