Disney recently released the most up to date official MCU timeline. Loki takes place after the events of Endgame, which was clear at the beginning of the series. However! Chronologically, the events in WandaVision happen AFTER the events in the Loki series! That changes EVERYTHING!
The Nexus commercial in WandaVision episode 7; “A unique anti-depressant that works to anchor you back to your reality, or the reality of your choice.”
The similarities in Loki and WandaVision, where they draw parallels between order and chaos. The symbol on Agatha’s broach possibly being linked to the visions that Thor had in Age of Ultron. Lastly, now that we know the events of WandaVision happened after Loki, Wanda’s post credit scene where she hears her children makes a TON more sense!
So who has Tommy and Billy? Mephisto? Master Pandemonium? Ch’thon? Some other dark and/or evil entity? Remember, in the comics, Master Pandemonium and Mephisto both take Wanda’s kids. BUT Ch’thon is in another dimension, the Flickering Realms, which is (allegedly) in the vicinity of Earth. Before Ch’thon left Earth, though, he created the Darkhold, which is the book that Wanda is reading, imbued with all of Ch’thon’s arcane knowledge. He grants powers to those who use the Darkhold in exchange for their souls. However, I don’t think that would be what he’s after with Wanda. And now that the Multiverse is the real deal, Ch’thon existing in another dimension with continued influence on Earth isn’t that big of a stretch.
Another, rather unique theory I’ve read about and seen several YouTube videos on, is that the finale events of both Loki and WandaVision are synchronized. Timing within each respective finale is there; the scene when Wanda reveals that she placed the runes on the Hex to defeat Agatha coincides with He Who Remains, Loki, and Sylvie crossing the ‘Threshold’ where He Who Remains doesn’t know what will happen. I’m not sure how much stock I personally put into this theory, but it has some strong points. If you search “Loki and WandaVision Finale Synced” on YouTube, you’ll see the video espousing said theory.
As always, let me know your thoughts down in the comments!