A cool crossover could be a scenario where a member of the SGA team is framed for a crime on Earth. The NCIS team is assigned to the case, but as they dig deeper, they realize that there are alien elements at play. They then have to work with the SGA team to clear the name of the accused and also deal with the alien - related issues that are emerging.
Maybe there's a situation where an alien artifact is found on Earth that has a connection to Atlantis. The NCIS team starts investigating it, not fully understanding what it is at first. Then the SGA team gets involved because they recognize the technology. They work together to keep the artifact safe from various threats, both Earth - based and alien.
One idea could be to have a character from SG1 accidentally end up in the SGA universe and have to adapt to the new technology and threats there. For example, Jack O'Neill could find himself on Atlantis and his military tactics and dry humor would create interesting interactions with the Atlantis team.
Another way is to join fanfiction communities or forums dedicated to either SGA or NCIS. Ask the members if they know of any good SGA NCIS crossover stories. They might be able to recommend some hidden gems that you wouldn't find through a simple search. Sometimes these communities also have their own collections or libraries of recommended fanfics.
One plot idea could be a joint case where the NCIS team and the NCIS LA team have to work together to solve a crime that spans across different locations. Maybe a terrorist threat that has connections in both Washington D.C. (where NCIS is based) and Los Angeles.
A more complex idea could involve a threat that endangers both the NCIS world and the Twilight world. So, the NCIS team has to team up with the Cullens and the werewolves to fight against this common enemy. This would bring in all the action - packed elements from NCIS like investigations, shoot - outs, and also the supernatural elements from Twilight like vampire powers and werewolf transformations.
Another concept could be that one of the NCIS agents has a family member who is in danger because of a supervillain's plot. The Avengers get involved to protect the agent's family, but the NCIS team doesn't trust them at first. Gibbs would be very protective and suspicious. As the story progresses, they all learn to work together. Ziva could show off her combat skills to Black Widow, and they could have a friendly sparring match while sharing their combat experiences.
One idea could be that some of the NCIS agents are sent on a mission to a world that has similarities to the Naruto universe. They could team up with Naruto and his friends to solve a mystery that involves both their worlds, like a powerful weapon that could disrupt both dimensions. The NCIS agents would be shocked by the ninja skills and chakra usage, while Naruto and his friends would be intrigued by the advanced technology of the NCIS.
One idea could be that the NCIS team is investigating a series of strange murders that seem to have a supernatural element. They end up calling in the Winchesters from Supernatural for help. The two groups initially clash due to their different methods but eventually learn from each other and solve the case together.
One idea could be that a case in Hawaii has connections to a national security threat that NCIS is already investigating. For example, a suspected terrorist cell in Hawaii might be linked to a larger international network that NCIS has been tracking. Agents from both teams could collaborate, with the Hawaii Five 0 team providing local knowledge and the NCIS agents bringing in their expertise on international threats and military - related matters.
One idea could be that the teams are brought together to solve a case involving a military - related crime that has ties to Hawaii. Maybe a stolen military weapon is being sold on the black market there. The characters from Hawaii Five - 0 can provide local knowledge and connections, while the NCIS agents bring their expertise in military investigations. Another idea is that a Navy officer goes missing in Hawaii and both teams have to work together to find him. They might initially have some clashes in their working styles but eventually learn from each other.
One idea could be that the NCIS team is called in to investigate some strange magical occurrences in the wizarding world. Maybe they think it's some new form of high - tech weaponry at first but then realize it's magic. Another could be that Harry Potter and some of his friends end up in the NCIS world and have to work with the team to solve a mystery that involves both magic and muggle technology. For example, a dark wizard is using muggle technology to enhance his magic and they need to stop him.