[WARNING: Spoilers ahead for the Agents of S.H.I.E.L.D. season 3 finale.]
When the second season of Agents of S.H.I.E.L.D. ended, the series offered a number of hints as to what fans could expect from season 3. In fact, the season 2 finale introduced the storyline that found many Inhumans undergoing Terrigensis all around the world and planted the seeds for Daisy's (Chloe Bennet) team of Secret Warriors, both of which became major story arcs when Agents of S.H.I.E.L.D. returned. Additionally, the season 2 finale ended on the cliffhanger of Simmons (Elizabeth Henstridge) being dragged into the monolith, to where we now know to be the planet of Maveth, which eventually led to the introduction of Hive (Brett Dalton).
Now, the Agents of S.H.I.E.L.D. season 3 finale has similarly offered hints about what's to come when the series returns for season 4, which has already been ordered by ABC. The two-hour finale, 'Absolution/Ascension,' largely featured the S.H.I.E.L.D. team's battle to defeat Hive and thwart the evil Inhuman's plans, but the final sequences were dedicated to setting up what's to come on the show.
At the end of 'Absolution/Ascension,' Agents of S.H.I.E.L.D. features a six-month time jump to Coulson (Clark Gregg) and Mack (Henry Simmons) on a stakeout. It's soon revealed that they're on a mission to find Daisy, who has gone rogue and is using her powers to rob banks. (Her Marvel Comics codename, Quake, can be seen in the headline of a newspaper in Coulson's room.) Daisy, for her part, is still be dealing with the loss of Lincoln - and it seems she's also continuing to work on her powers, using them to evade her former friends.
It seems Agents of S.H.I.E.L.D. season 4 will pick up this storyline when the show returns, as Coulson and Mack continue to track down the rogue former agent. But, if Coulson's comment about calling "the director" is any indication, he may not be in charge of S.H.I.E.L.D. anymore. That begs the question of who could have assumed command of the organization - perhaps Nick Fury (Samuel L. Jackson) has resurfaced at this point in the timeline? Or S.H.I.E.L.D. has officially merged with the ATCU and Glenn Talbot (Adrian Pasdar) is in charge? Maybe Melinda May (Ming-Na Wen) has taken over while Coulson searches for Daisy?
The final scene of 'Absolution/Ascension,' however, offers a different kind of storyline that fans can expect to see develop in season 4. The scene depicts Holden Radcliffe (John Hannah) finalizing a project with the title "LMD," which is the shortened name of Marvel Comics androids called Life-Model Decoys. In the comics, the LMDs were developed by S.H.I.E.L.D. to take the form of a person and act as a body double; the most notable LMD is of Nick Fury.
However, while the LMDs were created with good intentions - just as Radcliffe intends for "Ava" to prevent the death of anymore S.H.I.E.L.D. agents - the technology was known to go rogue on a number of occasions. So, with Hydra dismantled and Hive defeated once and for all, the final scene of 'Absolution/Ascension' positions the LMDs, and perhaps Radcliffe as well, as the potential main villain of season 4. Perhaps the scientist will learn the same lesson that Tony Stark (Robert Downey Jr.) did with his creation, Ultron, on the film side of the Marvel Cinematic Universe.
At the very least, given the focus of the last few sequences in the season 3 finale, it's clear that Agents of S.H.I.E.L.D. season 4 will deal with both Radcliffe's LMD and Daisy's defection from S.H.I.E.L.D. How these story seeds play out in season 4, though, remains to be seen when Agents of S.H.I.E.L.D. returns.
Agents of S.H.I.E.L.D. will return for season 4 in the fall on ABC.