Perhaps in the fanfic, Arcee's pregnancy is the result of some experimental technology gone wrong. She has to figure out how to reverse it or come to terms with it. Along the way, she teams up with Bulkhead. Bulkhead, being a gentle Autobot, helps her understand the value of new life. They face challenges from both Autobots who are skeptical about her condition and Decepticons who see it as a weakness to exploit.
It could be a long - lost Autobot that Arcee had a connection with in the past. Maybe he sacrificed himself in a previous battle, and his energy somehow remained and combined with Arcee's in an unexpected way, leading to the pregnancy.
One possible plot could be that Arcee discovers she is pregnant through some strange energy or experiment gone wrong. She then has to hide it from her Autobot comrades at first because she's not sure how they will react. As the story progresses, she might face challenges in protecting herself and the unborn entity from Decepticon threats.
You can start by looking on Archive of Our Own (AO3). It has a large collection of fanfictions on various topics including Transformers. Just use the search bar and type in relevant keywords like 'Transformers Prime Arcee pregnant'. Another option is FanFiction.net, but AO3 generally has a more inclusive and organized tagging system for finding specific types of fanfiction.
One possible storyline could be Arcee teaching Jack some combat skills that are unique to the Transformers. Since she has a lot of battle experience, she could pass on her knowledge to Jack, who is eager to learn more about the world of the Transformers and how to better protect his friends. For example, she might teach him how to spot weaknesses in a Decepticon's armor.
I'm not sure if there is a specific fanfiction about Transformers Prime Arcee being pregnant. Fanfiction can cover a wide variety of topics, but this one might be a bit of a niche concept. You could try searching on popular fanfiction websites like Archive of Our Own or FanFiction.net to see if any such stories exist.
It could also be that Arcee is injured herself and in a state of confusion and pain. Her sensors might be malfunctioning, and she mistakes Jack for an enemy. Jack, being the brave human he is, tries to help her but she lashes out at him in her disoriented state.
In a fanfiction plot, it could be that Megatron captures Arcee with the intention of using her as a bargaining chip. But during her captivity, he becomes intrigued by her spirit. He begins to have conversations with her, which gradually turn into a strange form of friendship. This friendship then starts to develop into something more, causing chaos among both the Autobots and the Decepticons as they try to deal with this unexpected relationship.
One great fanfiction could be about Optimus and Arcee going on a dangerous mission together. They face numerous challenges, like battling a powerful new Decepticon. Their teamwork and trust in each other are put to the test. Arcee's speed and agility combined with Optimus' strength make them a formidable duo. Along the way, they might have some deep conversations about the future of their race and their place in the war.
In some fanfictions, it could be that Arcee is kidnapped because of a personal vendetta. There might be a character, either a new creation or an existing one from the Transformers Prime universe, who has a grudge against her. Her fellow Autobots would then search high and low, using their detective skills and combat abilities to find and rescue her.
A likely kidnapper could be Starscream. He's always looking for ways to gain an advantage over the Autobots and Arcee would be a valuable hostage. He might think that by kidnapping her, he can force Optimus Prime to make concessions or reveal secrets.