Beware of Length
1. TFA- Optimus Prime from the current is somehow a resurrected/reborn/reformatted version of an Optimus from the Great War. Upon gaining of the matrix at the end of the series he gains awareness of his former life. The angst in this would be incredible seeing that he has lost both Ariel and Dion not once, not twice, but going on a total of three times. While Sentinel is still present with no memories of his own to justify Optimus's claims of their long existing friendship, the claims are dismissed.
Ultra Magnus being true to his G1 counterpart never truly wanted leadership but when it was trust upon him took it, now wounded and unable to continue his duties, sees this as an opportunity to return the true, 'Magnus' to power and instates Optimus, now aware of his rightful place, into power.
2. (I actually stated writing this and got no where, slowly) TFA- All along Ultra Magnus had backed Optimus as his next successor, when Optimus fell from graces roughly 1000 stellar cycles due to Elita and Sentinel's escapade, Ultra Magnus decided he was going to stay in power as long as he could in hopes that the now Prime, Optimus could somehow redeem himself. In this time the Council, and its Main figure Alpha Trion search out their own hopeful finding one in young Hot Rod, who they influence into entering the Autobot main forces since that is seeming to be a requirement for one to become Magnus.
The reason the Council took this action was it was clear that Ultra Magnus's stubbornness to regards to an heir could leave them with potential a grab for power if something does happen, as eventually did happen, and the hope to have a Magnus that is more sympathetic with civilian strife, and perhaps less inclined to continue to ramp up the military.
At present Optimus Prime returns to Cybertron a victorious hero, Megtron captive, Allspark returned, Matrix recreated, redeeming himself beyond what any of the Council could have imagined. They can no longer deny Ultra Magnus's request to have Optimus succeed him although Optimus was not accepted by the Matrix as a proper Magnus would be. See the wiki for a nice picture of his hang from around his neck.
Now, the Council has to figure out how to use their own candidate, since now they are unable to elevate him as they had planned. With Ultra Magnus compromised as he was at the end of the series they decided to award Rodimus with being placed as Head of the Guard to the former ruling Magnus. This position places their candidate in a position between the New Optimus Magnus and the Old Magnus who would serve in a advisory role for the rest of his existence.
Rodimus who had been working his entire career to possibly achieve Magnus experience this let down but with his soldier's fortitude does the job asked of him although he has a certain bitterness toward Optimus. He realizes that while Optimus has the one thing he strived for, that he can limit Optimus's access to the wisdom of Ultra Magnus one of the things that Optimus would want in his early days as ruling Magnus.
( Oh Lordy, long bunny)
This eventually grows as struggle, in which Rodimus becomes fiercely jealous of the time the two Magnus's spend together and Optimus being relatively oblivious to this just doesn't understand and tries to schedule none the less.
From here the bunny grow vague but picks back up with Rodimus being blatantly informed of his Council's puppet status by an agitated Ultra Magnus during a verbal spat about Ultra Magnus's favorite Optimus. After which Rodimus storms out, ends up piecing together facts and realizing that everything from his joining the military, to his quick advancement to the academy, his early graduation, and his title of Prime, as well as even Council material Red Alert being assigned to his team was potentially all fabricated to make him appear as a rightful replacement for the chosen candidate in the optics of the populace. Returning to Ultra Magnus in the middle of a meeting between Optimus and Ultra Magnus he submits his resignation as Head of the Guard with Ironhide taking his place, and as Prime, and walks out joining the civilian caste from which he came once more.
Remnants of the Decepticon forces carry out an attack on the Council Chambers while the Council is in session and killing several members including Alpha Trion. With the Council in disarray without the steady presence of Alpha Trion, Optimus steps down from the position of Magnus, a position he never found himself feeling comfortable in, to away him to be eligible in the election of the new Head of Civilian affairs. His spark lies with the people of Cybertron but never with the warhawk tendencies of the position of Magnus. After informing Ultra Magnus of his decision, Optimus has the Elite Guard hunt out the Council's choice for Magnus, Rodimus, in Hopes that the former Prime would still be willing to consider the position.
Rodimus, now going by his recruit name of Hot Rod is living with his retired boot camp drill sergeant, Kup, that has been trying to convince the younger mech that "While yes the Council may have been watch, and may have tugged a few strings, that heroism is still heroism," and for Hot Rod to get his aft back there and grow some back struts. Ratchet being back on Cybertron and in place as Physician to the current Magnus, as well as well acquainted with Kup from the Great War knows of Hot Rod's location, and after there seemingly being no trace of Rodimus, decides to venture to the fellow veteran's home to bring the runaway Candidate back himself.
Due to some great argument of Ratchet's? Rodimus goes with the medic back to Magnus estate where they are greeted by Optimus, an accepting of the situation, if not somewhat oddly amused Ultra Magnus and several Council member. In a seeming whirl they organize the accent to Magnus for Rodimus, during this process at some point he's handed the matrix, probably in a 'here hold this for a picture' fashion, which accepts him and reformats him into a proper Magnus. Thus proving that although the Council may have selected and groomed him to be Magnus, Rodimus to his core, title or not, was the rightful heir.
This creates a delightful bit of mimicking of succession between Optimus to Rodimus, and ends up making everyone happy. Optimus a War Hero as Head of Civilian Affairs, and Rodimus, who came from civilian ranks rising to Magnus, a nice slightly mimicking of the Prime and Lord Protector roles that were in Bayverse.
Should I mention this started as a prompt for Ultra Magnus/Rodimus Prime and grew into a monster?
3. G1- Punch torn between Soundwave's influence trying to put Counterpunch as his main personality, and an undecided, up to the taker of the bunny, Autobot trying to negate the affect of Soundwave's actions, maybe Ratchet, maybe fanon shrink Smokescreen? Either way basically a duel romance between Punch/Autobot and Counterpunch/Soundwave would occur as more and more drastic methods would have to be implemented in the fight for the spy's soul, so to say.
4. TF: Prime- Wheeljack discovers a group of processor damaged Autobot Explorers on some jungle world, these poor unfortunate mechs are the dinobots. They have forgotten their Cybertronian names, ranks, lives, but their natures are still present.
Now if one were to continue this bunny past the discovery of the Dinobots, Wheeljack knows he could abandon the mechs their, allow them to continue their existence as they had been but his morals keep him from doing so. This could start off a series of miscellaneous Wheeljack and Dinobot vs the 'Cons and the Universe adventure set.
5. TFA- Lockdown only once had an apprentice, that mech's name being Axor. For the sake of the bunny you'll have to run with me here.
Axor from 2010 Bayverse toylines looks like a white and blue Lockdown, Axor in name pays homage to Axer from RID who has a toy that looks somewhat remarkably TFA Prowl like, at least to me
Link Provided: http://tfwiki.net/w2/images2/thumb/9/97/Axer_rid.jpg/800px-Axer_rid.jpg
So let's say Axor his apprentice originally looked very similar to Prowl. In his ambition, and also Lockdown's mutilation fetish, over time the mech was reformatted to be basically a miniature Lockdown. Due to Axor's youth, and emerging mental instability he turns on Lockdown and they become enemies.
The twist here is
A.) Prowl is Axor who after gaining some semblance of sanity back, most likely through being a cyberninja, got himself altered back to his original form and when he runs into Lockdown he has to fight everything in him so as not to return to what he once was, maybe with nice little crazy Axor talking in the back of his Processor
B.) Lockdown takes in Prowl's coloration and build and decides to have a go at having an apprentice once more, only this time he's found a more stable mind to work with.
C.) Prowl becomes Axor- this would have to be AU of course.
D.) Prowl is Axor, downgrading himself to get close to his target Ratchet, waiting for his time to kill the older mech, but slowly finding his life with the Autobots to be something greater than the bounty, but when Lockdown arrives on the scene he must make his choice, Keep living the life of Prowl the mech with a future, or Axor the mech with only a long, sad, disturbed past.
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Alright I'll leave those five to the masses.