Odo finds his new role fulfilling as it satisfies his innate sense of order. Still an outsider with little status, he has no fear about sounding off on Cardassian injustice on Bajor. Dukat is willing to risk the occasional instance where Odo's impartiality and is quick to respond to any problems. Few criminals escape his notice. Conflicts with Cardassian political interests on the station. With his reputation aboard the station established, Odo was sought out by the station's prefect, Gul Dukat, who recognized his potential as a criminal investigator. For his first case, Dukat requested that Odo find and arrest whoever was responsible for the murder of the station's Bajoran chemist, Odo was initially hesitant in taking on the case. He said he was no investigator, but Dukat succeeded in changing his mind by suggesting that if Odo did not take the case, he would have to resort to the traditional Cardassian method of searching out criminals: rounding up and killing 10 Bajorans at a time until the culprit came forward. Kira warned him that, even unofficially, he was working for the unjust Cardassians. Odo insisted that he was not working for Dukat, just trying to solve a murder. No culprit was arrested in relation to the murder at the time, but Gul Dukat was sufficiently impressed with Odo's investigative skills.

He has extraordinary awareness of detail, which seems to be related to his ability to change shape, and maintains contacts in the Cardassian hierarchy that enable him to uncover vital information that would not be available to a Federation or Bajoran officer. Odo is more than willing to bend the rules to do his job, and plants a number of hidden surveillance devices on the station. He pays particular attention to Quark, the station's Ferengi barman, who often engages in illegal activities. Odo also uses his shape shifting abilities to conceal himself, gaining priceless information. He makes a careful study of all new arrivals to the station, ensuring that nobody with a criminal record escapes his notice. He is exceptionally thorough and, as a matter of course, never accepts the first explanation offered to him. Even when he temporarily loses his ability to change shape, Odo continues in his post and proves that his other abilities make him more than equal to the job.

Odo shares a very complex relationship with his people, the Founders. He was one of 'the hundred' infants sent out into the Galaxy over the years to make contact with other species and report back to the shapeshifters. Odo was found in the Denorios Belt, and matured on the planet Bajor, all the while wondering who or what he was. Throughout his career as chief of security aboard the station Deep Space Nine haunted by this mystery. Odo believes the answers to many of his questions are on the other side of the newly discovered Bajoran wormhole. In 2371, he joins the U.S.S. Defiant expedition into the Gamma Quadrant and feels an odd compulsion to visit the Omarion Nebula. Arriving there, he is overwhelmed to finally meet his people.

He nevertheless resolves to aid the Federation in its cold war against the Dominion. He travels to Earth for a comprehensive debriefing in mid-2372, and helps Starfleet conduct phaser sweeps to detect Changeling infiltrators. A direct conflict of interest is inevitable, and Odo becomes the first Changeling to kill another. He pays the price for this a year later, when the Founders afflict him with a debilitating illness that forces him to return home and face judgment. His punishment is to be cast out of the Great Link and made a 'solid.' The condition is reversed some six months later, when a dying infant Changeling links with him.

The unexpected arrival of the female shape shifter further fuels Odo's indecision. She feels the need to be with one of her own, after being around 'solids' for so long, and Odo secretly feels the same. Despite the fact that the Dominion is waging war against his adopted home, he is swayed by some of his fellow Changeling's arguments that he does not belong. He admits that he often thinks about the Great Link. The female shape shifter offers him clarity in the form of a link, and Odo goes against his promise to Kira not to do so. He tells himself that by linking he may be able to convince his counterpart that the Federation is not a threat, but whether he truly believes this is uncertain. The offer certainly proves too tempting to resist.

Kira angrily tells him he has handed the Alpha Quadrant to the Dominion on a plate, but he says nothing else seemed to matter but the link. Odo only becomes troubled when he witnesses first hand the female shapeshifter's ruthlessness. On hearing about Starfleet's battle to retake Deep Space Nine, he realizes that there are people fighting and dying for something he believed in - people who used to be his friends. Odo tries to tell himself that the link means more to him than solids, but he cannot bring himself to believe it. The moment of truth comes when Odo is told that Kira has been arrested, and will be found guilty and sentenced to death. His course of action abruptly becomes clear; he organizes a team of Bajoran deputies to help the liberated Kira and her resistance cohort, the Ferengi Rom, reach the station's main computer and shut it down.