This falls under the "In the Name of Science" side quests questline. The first is attacks on caravans which occurs fairly early.
The last three "At the Heart of the Rebellion", "Doctor Asili's Experiments", and "The Trial" can be difficult because there is never any indication that these quests are available.
With that said anytime after
if you go see the Governor of Hikmet, you can start "At the Heart of the Rebellion", which naturally progresses through the other two.
The choice that didn't matter, which you might think it does is:
The choices that mattered in order to get a "Friendly" reputation seemed to be during "Doctor Asili's Experiments":
After the rebellion quest I was actually still "suspicious" with the Alliance so don't worry about that because, if done right, "The Trial" will make up for anything you lost, pretty sure I was still suspicious going into the trial too.
During "The Trial": Just collect every piece of evidence. After I collected every piece of evidence and convinced everyone to testify, it looked like it glitched but it isn't, you just need to go talk to the Prosecutor to continue the quest, idk why it doesn't tell us but that's the next step.
After you talk with the prosecutor and the Governor, you'll get a +3 then a +5 and it should pop! Mine popped after the +3 but if you ticked off the Alliance more than I did it might take the +5.
Edit: If you want to convince