One idea could be that while Tony is sick, the team has to handle a crucial case without his usual on - the - ground assistance. They struggle at first but then find new ways to work together. Tony, from his sickbed, still manages to offer some key insights through phone calls or video chats.
Maybe Tony's sickness is not just a normal illness. It could be related to a case he was working on previously, like he was exposed to some strange chemical or virus. The team then has to race against time not only to solve the case but also to find a cure for Tony. His illness also makes him more vulnerable and reflective, leading to some deep character development.
Another idea is that Tony is injured while rescuing a kidnapped child. He gets stabbed in the process. His injury makes the NCIS team more determined to catch the kidnapper. During his recovery, Tony forms a special bond with the rescued child, which is a new and heart - warming aspect of the fanfiction.
One plot idea could be that Tony and Ziva are trying to raise their baby while still being involved in NCIS cases. They might have to deal with danger that comes too close to their family. Another could be the baby having some sort of special ability that they need to protect from bad guys who find out about it. Maybe the baby's birth also brings some old enemies of Tony or Ziva back into their lives, creating a whole new set of challenges for them.
Well, perhaps they are undercover in a foreign country. They have to blend in with the local culture, which leads to some humorous situations like Tony trying to learn the local dance or Ziva struggling with the language but still managing to intimidate people. And then there's the danger aspect, where they discover a terrorist cell operating within the city they are in and have to stop them without blowing their cover.
One idea could be that they initially struggle with the news. Tony might be over - the - moon but also worried about the dangers of their job affecting the pregnancy. Ziva could be more reserved, fearing how it will change her life as a once - tough agent. Another plot could involve their team members' reactions. Gibbs might be secretly happy but also strict about safety protocols at work. Abby would be all excited and start knitting baby clothes right away.
Abby would be all over Tony, bringing him some of her special energy drinks (even though they might not be the best for a sick person). She'd also use her skills to try and find out what's wrong with him in a more scientific way. Ducky would of course offer his medical expertise, and might even tell some long - winded stories while examining Tony to try and keep his spirits up.
In a more comical fanfiction, Tony could be tape - gagged by a new agent who mistakes him for an intruder. The rest of the team then has to deal with the chaos that ensues as they try to figure out what happened and why the new agent took such drastic action. Tony, of course, is frustrated and can't wait to get the gag off and give the new agent a piece of his mind.
Perhaps Kensi is infiltrating a criminal organization. During the process, she is discovered and tortured to get information out of her. She gets bruises and some serious internal injuries. Her team races against time to find and rescue her. Once they do, they have to deal with the aftermath of her trauma both physically and mentally.
One possible plot twist could be that the shooter has a personal vendetta against Gibbs that dates back to a case that Gibbs thought was long closed. Maybe the shooter was wrongly accused in that case and has been planning revenge ever since.
One plot idea could be that Hamilton's illness makes him reevaluate his relationships. He might realize who his true friends are as some people visit him often while others avoid him. Another could be a time - travel twist where in his feverish state, he dreams of different outcomes in the revolution. Or perhaps his sickness spreads in the community and he has to take on a role of guiding the prevention efforts despite being ill.
Another theme could be Tony's vulnerability. When he's sick, he's not his usual confident self, and this can lead to some character development. Writers often explore how he copes with being weak and relying on others.