Mass Effect's Andromeda Initiative set out for a whole new galaxy, intent on paving the way for the future of the collective races from the Milky Way. Their mission was clear, and their scope was massive, but one thing they hoped would work itself out on its own were the prejudices that had developed over centuries in their home galaxy.
Unfortunately, too many wars bred mistrust, skepticism, paranoia and doubt in the Milky Way. While the founders believed they could get past those prejudices through their conjoined efforts to start anew, it was impossible for many to let go of the past. Upon arrival in the Heleus Cluster, the Andromeda Intiative's Nexus space station met with the Scourge, and the impact saw a number of its high-ranking officials killed.
Many individuals in positions of power were lost, and the survivors had to comb through the dregs to determine who would take over as Director of the Initiative. Many disagreed with the only option they seemed to have left, as Salarian accountant Jarun Tann was in no way cut out to be a leader. The Initiative's Deputy Assistant for Revenue Management had neither the credentials nor the personality for the position, but with no one else left, Tann grabbed onto the position and refused to let go.
There were a number of reasons Tann was unqualified for the job, first and foremost being how deviously he skirted around issues of pre-existing prejudices on his applications when joining the Initiative. Considering he (at the time) seemed incredibly unlikely to assume a position reliant on people skills, those issues were apparently overlooked. No one could have predicted the tragedy the Initiative would face upon arrival in the Heleus Cluster, but had they considered all potential outcomes -- and the possibility of losing so many leaders -- they might have paid more attention to Tann's unwillingness to talk about his hatred for the Krogan.
Salarians and Krogan have a long and troubled history in Mass Effect's lore. It was the Salarians who provided the Krogan with the technological advancements that contributed to their evolution as a race, and the offering of a new home planet was just the icing on the cake. Unfortunately, the Salarians didn't do those things because they wanted to make friends. Their efforts were an underhanded attempt to pacify the Krogan, earn their trust and eventually convince them to exterminate the Rachni for the rest of the galaxy.
After the Rachni Wars, the Krogan spread all through Citadel Space, their numbers ever-increasing and their capacity for conquest and violence troubling to the other Citadel races. Eventually, the Salarians and Turians combined their efforts to stop the Krogan once and for all with genetic weapon designed to infect the Krogan with a virus that would significantly curb their reproduction.
The animosity that resulted from this attack and successful attempt to control the Krogan bred a deep-seated hatred on all sides that the Salarians and Krogans clung to even after departing for Andromeda. Because of the Krogan's war-faring and violent nature, they were not initially offered a seat on the Initiative's Nexus Council. Shortly after Tann took power on the Nexus, an uprising resulted as fear and uncertainty spread through those who'd been woken from stasis.
Tann decided to wake the Krogan and use them to put down the rebellion. The Assistant Director of Colonial Affairs, William Spender, promised the Krogan that, if they put down the rebellion, Tann would grant Clan Nakmor a seat on the Nexus Council. Tann was infuriated when he found out about Spender's offering, and he refused to budge. Spender reneged on his promise to grant them equal power with the other races -- even though Clan Nakmor did what they were asked to do.
Enraged, clan leader Nakmor Morda wanted to crush Tann and Spender both, and with good reason. Yet again, the Krogan had been manipulated by Salarians to do their bidding, only to be discarded once they'd done the deed. Nakmor Kesh intervened before it got out of hand, convincing Morda not to react to Tann the way they may have in the past. After all, this was a new galaxy and a new chance for everyone.
Instead of crushing Tann, Morda gathered the members of Clan Nakmor, and they disembarked from the Nexus. Intent on starting a new life in Andromeda without the influence or dictation of the Andromeda Initiative, Clan Nakmor started an independent colony on Elaaden they named New Tuchanka. Kesh remained behind on the Nexus to maintain contact and continue attempting to restore relations between her clan and the Initiative, but Clan Nakmor had no intention of giving the Initiative another chance.
It wasn't until Pathfinder Ryder arrived that a new opportunity arose to restore relations between Clan Nakmor and the Initiative. Tasked with recovering a stolen Remnant drive core, Ryder could return the drive core to Morda, who then allowed them to set up an Initiative outpost in New Tuchanka and begin repairing relations between the Krogan and the Nexus.
The Andromeda Initiative's rush to leave the galaxy after the threat of the Reaper invasion was revealed perhaps forced them to cut a few corners when it came to mending rifts between the races. Fortunately, the player character was offered opportunities to do what the Initiative itself wasn't given time to do. Whether the Krogan of New Tuchanka and the Initiative can truly mend their fences is undetermined, but one can only hope that issues resurfaces in the next Mass Effect game.