"NCIS" is known for having a cast of characters that seem to be particularly talented at failing in relationships, and Ellie becomes a member of this group in Season 13. The choice to have the character go through a divorce makes perfect sense given the stress and distance the couple goes through, and of course there's Jake's affair. But one of the biggest reasons that Ellie and Jake split up is the realization that they really don't have that much in common.
The couple meets while they both work at the NSA, and their jobs and devotion to the organization is what brings them together, and keeps them together. When Ellie decides to transition to the NCIS, she likely thinks that her marriage can handle it, as it's just a new job. But once she starts working with new people, and not with Jake, Ellie starts to realize that maybe the NSA is all she really has in common with her husband, and that's definitely not enough to keep a marriage stable.
In an interview with Entertainment Weekly directly after the 2015 episode in which Jake reveals his affair, Wickersham spoke about the fate of their marriage, stating that the inability to share all the details of her work at NCIS with Jake definitely factors into Ellie's divorce, but that "in reality, that shouldn't end a marriage, so I feel the marriage, the foundation, wasn't strong enough to begin with." Thankfully, the divorce allows Ellie to fully devote herself to her job at the NCIS, meet new people, and start a new chapter in her life.
