How I feel Halo 5 will be along the lines.
The emptiness without Cortana
During the last fleeting moments with Cortana who sacrificed herself to protect John from the nuclear explosion, he came to realize he developed feelings for her. Even though she is a A.I. and he is a super soldier, basically a human, he isn't immune to feelings. It is these feelings that will cause him to refuse any other A.I. to replace her, letting his emotions decide his actions, which makes him less than combat ready for any missions.
Bursts of Information
Fleeting familiar data bursts randomly are picked up by infinity and her crew all over the galaxy, much like Promethean Knights from before, but the data bursts are much different than before analysis which leads to the assumption of new tech is activating. UNSC then orders Infinite to investigate the source of these data bursts, which leads to the discovery of new types of promethean enemies that been activating, leading to new type of threats. He isn't alone in investigating the new types of threats, where he runs into his old ex-nemesis and greatest ally, the arbiter who is currently leading his species.
Together they venture deep inside the planet, where John discovers that Didact wasn't the only promethean to harbor hatred towards humanity. This new face has the backing of an breakaway faction of Prometheans who are raising an army to destroy humanity. John and Arbiter must escape once the faction notice them here, quickly they flee through the caverns towards their respective ships. Arbiter orders majority of his fleet to stall the impending invasion of Earth as Infinity, her crew, and arbiter make a bee-line towards Earth.
Once Home, Now Gone
Arbiter's fleet did little to stop the invading force of Prometheans. They quickly catch up to infinity and surround her in orbit above Earth. Outgun and outman, Infinity is toren to shreds and crash lands into the Desert, creating massive crater which is quickly surrounded by Prometheans. Jumping to action, John and Arbiter safely escort remaining UNSC personal and VIPs to safety as they fight their way through the battlefield. Symbolic stand, Arbiter decides to stay with the remaining UNSC forces and elites to battle against this threat.
After escaping, they soon realize that Earth is being scored clean, whole cities and civilizations being wiped out by orbiting Promethean ships. Earth is now completely stripped away, leaving only global desert and crystallized alien landscape. Johns manages to hold out, they manage to avoid being reduced to dust and found safe heaven. The remaining UNSC forces and humans go into hide, so does John, relying on his armor to defend the remaining pockets of resistance. Years pass as they repeat hide and run tactics, trying to weaken the enemy that seems to have no end in sight. This goes on until he gets help from a familiar source, an familiar voice he once thought was gone. This voice tells him he must search for her, for she holds the key to stopping the Promethean's Revenge against humans...
Now this is a dark storyline fit for the second chapter of desperation and hope.