Well, it could have the Doctor teaming up with the Autobots to save the universe from a time-traveling Decepticon threat.
The Doctor could accidentally land in a battle between Autobots and Decepticons and end up helping one side while trying to figure out how to restore the balance of time and space. Another possibility is that a powerful relic from another dimension attracts both the Doctor and the Transformers, leading to an adventure filled with mystery and danger.
One storyline could involve the Doctor getting stuck in the Transformers' world and having to use his wits and the TARDIS to find a way back home while helping them in their battles. Or maybe there's a glitch in time that brings Transformers to the Doctor's universe, causing chaos that only they can fix together.
Often, such crossovers might have Merlin using his magic to assist the Doctor in facing interdimensional threats. Or, the Doctor could travel to Camelot and encounter Merlin's challenges. There could also be time paradoxes and alternate timelines explored.
The key elements could include interactions between the characters from both shows, maybe a shared adventure or a mission to save the universe. Storylines could involve time travel paradoxes or facing a common enemy.
One interesting storyline could be the Power Rangers and Transformers teaming up to fight a common enemy that threatens both their worlds. Maybe a powerful alien force that can corrupt technology and has the ability to create its own powerful monsters. The Rangers' martial arts skills combined with the Transformers' brute strength and advanced weaponry would make for an epic battle.
Well, one way could be that the Jewel of Four Souls in Inuyasha's world has some sort of energy that the Transformers are interested in. Maybe the Autobots want to protect it from the Decepticons who see it as a powerful energy source. Inuyasha could initially be hostile towards the Transformers, thinking they are some new kind of demon. But as they prove their good intentions, they could team up. Kagome could also use her spiritual powers to help the Transformers in some way, like healing their wounds if they get damaged in battles against the Decepticons.
There could be one where the human tries to understand the Dalek's motives and find a way to peacefully coexist.
If Jack is a Star Killer, perhaps he has a vendetta against a certain group in the Transformers world. Maybe he blames them for something that happened to his family or friends. His actions as a Star Killer could start a chain reaction of events, leading to a full - scale war. The Autobots would have to figure out a way to stop the war and also get to the bottom of what's driving Jack to such extreme actions. They might try to reason with him or use force if necessary.
One possible storyline could be that Bumblebee was exposed to a strange energy source that caused an unexpected biological change, leading to pregnancy. He then has to deal with the reactions of his fellow Autobots, some of whom are confused and others who are supportive. Another storyline could be that an enemy has somehow engineered Bumblebee's pregnancy as part of a devious plan to either weaken the Autobots or create a new type of weapon using the new life form.
Well, you might see characters from both universes teaming up to face a time-traveling threat that affects both Zootopia and the Doctor's world. Or, it could focus on the cultural clashes and similarities between the two very different settings.
Often in such crossovers, you'll see unique mash-ups of technology and gadgets from both shows. Storylines might involve saving a planet that's at the crossroads of Star Trek and Doctor Who's timelines. Also, there could be fun character interactions as they face challenges that require the combined skills and knowledge of both crews.
One possible storyline could be that Madara, with his godlike powers, tries to find a way back to his own universe. Along the way, he meets characters from the new universe who either help or hinder him.