Jake and Holt's relationship on Brooklyn Nine-Nine was one of the best on the show. It evolved from one between a strict police captain and his immature, but mostly brilliant subordinate to a father-son-like relationship. Holt's robot-like demeanor and Jake's daddy issues that led to his attachment to him were key elements of their interactions and also the cause of disagreements between the two from time to time.
A lot of their clashes happened in the earlier seasons when the two were still getting to know each other and both were trying to get the other to bend to their will. Most of the terrible things they did to each other resulting from these disagreements happened in the workplace, but there were also times when they crossed boundaries and messed up each other's personal lives.
When Jake Disobeyed Holt's Orders During A Case
Jake disregarding Holt's orders while working a case happened several times, but the most notable was in the episode, "The Chopper." Jake was convinced they had a major case when one of the thieves from a group called The Fulton Four was murdered but Holt told him not to get overexcited about it, especially when Wuntch showed interest in it. Instead, Jake got a chopper for the case, but thanks to that, they recovered the stolen 21 million dollars. Wuntch took advantage of that to send Holt to the Public Relations office at the end of the episode.
Contrary to Holt's orders, Jake made a spectacle out of the case, leading to him being sent to a desk job he hated. His position as the captain of the Nine-Nine was important to him because it was his first command after a long time of being marginalized and side-lined. So, his transfer to the P. R. office really hit him hard, especially with his nemesis, Wuntch, humiliating him all the time.
When Jake Was A Horrible Boss
While Jake and Holt were in witness protection in the episode "Coral Palms Part I," Jake started secretly investigating Figgis, despite warnings from Holt and the marshall not to. In retaliation for Holt taking away his file with information on the case, Jake took a job at the Fun Zone as the manager, a position Holt had been working for, and gave him difficult tasks.
Holt was only trying to make the best of their situation by getting a job and aiming for the managerial position, but Jake's actions were out of spite and a way to blackmail Holt into giving back his files. His actions also led to the recording of the video that they ended up using to lure Figgis to them, putting their lives in danger.
When Holt Gave Jake's Case To The Vulture
While Jake was working the Lincoln Street Murder case in "The Vulture," he was called back to the precinct, where Holt handed his case over to the Vulture. Despite Jake's protests, he obeyed Holt's orders and gave the Vulture the file, but later worked the case secretly with the rest of the squad to "out-Vulture" him.
Holt was the worst here, as he disregarded the work Jake had done on the case so far when he ordered him to give it up., especially considering that the Vulture was notorious for swooping in at the last minute to take over cases when they were close to being solved and claiming all the credit. Granted, Jake was partly to blame for not involving the whole squad from the beginning, as he wanted the glory of solving the case for himself.
When Jake Mocked Holt's Dresscode Orders
When Holt first joined the Nine-Nine, he asked everyone to wear a tie. Jake was against this new policy and kept showing up without one and disobeying several orders related to the case he was working on at the time. As punishment for his actions, Holt assigned Jake to work in the records room. When he went to check on him later, he found him having completed the work and finally wearing a tie. However, he also had no pants and was wearing a speedo instead.
Jake's childish behavior was set up as a joke throughout the show, but it was understandably frustrating for Holt, considering how he'd struggled to get his first command and simply wanted to show that he was capable of handling it and gaining the respect of his subordinates.
When Holt Undermined Jake In Front Of A Perp
One of the most memorable guest appearances on Brooklyn Nine-Nine was in the episode, "The Box," when Sterling K. Brown played Phillip, a perp suspected of killing his dental practice partner. Jake was interrogating him and Holt decided to join him then later mocked Jake when he couldn't get Phillip to confess. Eventually, Jake managed to trick the perp into confessing to the crime, impressing Holt.
Holt and Jake's father-son dynamic resulted in him often needing Holt's approval, so his belittling of him during the interrogation messed with that and his self-esteem. He ended up doing crazy things, like the guitar strum and scream, to get Phillip to confess, which just made him get laughed at more and feel worse.
When Jake Took Kevin Out Of Witness Protection
After Holt double-crossed Seamus with the help of the squad in the episode, "The Favor," Seamus threatened to harm Kevin, so Holt sent him into protective custody with Jake as his guard. Over time, Kevin felt suffocated in the house, where Holt ordered them to not even open a window or ever go outside. In trying to keep the peace, Jake secretly snuck Kevin out to the library, but Holt found out and followed them, along with some of Seamus' men.
While Jake had noble intentions, his decision to go against Holt's directive was reckless and could have cost Kevin his life. Their trip resulted in Holt's capture, but they were fortunate and managed to save him in time and stop Seamus once and for all.
Holt's Reason For Choosing Jake As His Security Detail
In the episode, "Christmas," Holt received death threats, so the deputy chief insisted on security detail. Holt chose Jake because he didn't believe the threats were real and thought Jake wouldn't take it seriously anyway, like most of the things he does.
This was another case where Holt undermined Jake's abilities as a detective. Although Jake proved him right to some extent by doing several immature things while watching over him, such as handcuffing them together and throwing away the key, he took his assignment seriously and helped solve the case, proving that he was, indeed, the smartest detective on Brooklyn Nine-Nine.
When Jake Badmouthed Holt To A Reporter
While spending time with a former crime thriller writer, Jimmy Brogan, Jake got drunk and started complaining about Holt. Jimmy wanted to publish the terrible things he said, but Jake asked him not to. But Jake also punched him for what he said about Holt, resulting in Jimmy writing a scathing article about current NYPD officers and their methods.
Jake's behavior here was irresponsible, especially after Holt warned him of Jimmy's character and that drinking with him was not a good idea. It almost resulted in Jimmy writing a derogatory article about Holt, which may have negatively affected the career he worked so hard to build. It was also a sad moment for Jake on Brooklyn Nine-Nine, as he lost someone he idolized and credited for writing the book that inspired him to become a cop.
When Jake Meddled In Holt's Relationship With Kevin
Jake meddling in Holt's relationship happened several times - from the time he investigated why Holt was grumpy in "The Wednesday Incident," discovering that it was because he was attacked and stabbed (leading to a fight with Kevin) to his efforts to bring them together after they separated in the final season.
Most times, his meddling made things worse, although, to his credit, it also pushed them to talk things out and make peace. He often did this regardless of Holt's instructions to stay out of his personal matters and advice from his workmates, which was actually one of the defining aspects of his character.