Spoilerphobes be wary, as ever.
So the story starts with your character immediately being introduced to Havoc Squad, with their past training details - specifically what "qualified" them to be selected for/by Havoc - kept in the dark except for expository dialogue. Kudos to hitting the ground running in this regard, but it is slightly hard to feel invested when you know nothing of exactly what character traits you 'exhibited' which sat right with officials.
Having joined this elite squad, you spend your time being ordered around by an Ord Mantellian Lieutenant by the name of Aric Jorgan who has no formal connection to Havoc, whilst they themselves do something away from Fort Garnik. Such daring acts involve going to find a spy who is already dead - you get chastised for not being fast enough, and all this time there's an entire battalion of soldiers stationed outside this town. Wouldn't our innovative Sergeant or, dare I say it, some other Mantellian lackey just simply radio on ahead and ask these guys to scout the village? It is revealed after this that Havoc are trying to find this bomb which the Separatists stole, hence why they are more spread out than seemingly coherent. Regardless, it isn't all being by yourself. Needles, Fuse, and Wraith all help on separate missions, with Wraith even being present during an armed intervention and subsequent cutscene. Needles and Fuse simply talk, although Needles does send you on ahead to a nearby town with an antidote for acute radiation poisoning from the bomb.
Eventually the bomb is found and Havoc goes off the grid. As you are conveniently left behind, it's your job to go find both the bomb and Havoc; you find that Havoc are going rogue and are taking the bomb as a present for the Imperials. From here on out, it can be seen that the squad sends your character away to stop them interfering with their larger plans, and this does make a lot of sense considering that you were essentially forced onto them without any regards for concern. Also worth mentioning at this point: Ord Mantell provides perhaps the most difficult starter-planet mission, and it's all because you don't get your companion until you're about to leave the planet for the first time; whilst tearing through the entire Separatist Stronghold by yourself isn't an issue, I don't think anyone has gone into and come out of that first room where you realise the Imperials are on the planet without having died at least once. Perhaps with Disciplines allowing you to choose your advanced class without need for a trainer, this could happen, but I haven't tested it to see yet.
So you move on to Coruscant and meet General Garza, the woman responsible for managing Havoc Squad. She directs you to try to find one of Havoc's original members and mentors to the squad formerly known as "Havoc under Harron Tavus", Jek Kardan, who is conveniently on Coruscant doing deals with the Imperials who happen to be residing on the planet. Along the way you have to scrap resources and deal with the Senate who have caught the foul wind of Havoc's betrayal. Sadly, political dealings will occur more frequently later on in the story. After finding and stopping your target, you are pointed to an orbital station where Wraith is holding one of the Senators who requested an audience with you. This mission actually does have longer-term consequences, as you can either save the senator and let Wraith escape, or allow the Senator to die and kill Wraith.
So the prologue ends and you're off chasing down the other members.
The Trooper's mission on Taris is actually one of the more harrowing. Basically, Needles, the squad's former chemical expert, is experimenting on perfecting a version of the Rakghoul virus which could potentially be weaponised. Rakghouls in theory are terrifying; a creature which used to be sentient now unwillingly reduced to a primal beast by the transmission of a plague from an already-infected and transformed individual. The notion of this plague becoming weaponised and used against entire armies and even innocent civilians is just deeply unsettling. So thankfully Needles is stopped, but you then have the option of keeping his research to give to Republic scientists on Coruscant or just outright destroying it. Keeping such an abhorrent creation settles as well as the very idea of a weaponised plague in my eyes. Needless to say, I don't think I've yet come across anyone else on Taris who I was really pleased to have killed as I was with Needles.
Nar Shaddaa and Tatooine are actually both very interesting, as they both play with your expectations. Nar Shaddaa involves you working with the SIS and stopping a branch of traitorous Republic soldiers - no Havoc member this time - who are working with an incredibly patriotic Droid who is unaware of their evil intentions until you show up with your Havoc badge. All this while, you're trying to keep the desertion a complete secret from the SIS team watching your every move. Tatooine, meanwhile, sees demolition expert Fuse turn traitor again, but this time on the Imperials, having been sickened by their using his bomb designs on civilians. Whilst you are still pursuing him, it is now for a rescue as opposed to an outright immobilisation. Like Wraith, you have the choice to spare him and let another target escape or pursue the other and kill both. In this case, the Imperials set a self-destruct to blow up their base and try to flee with their bombs, and you unfortunately only have the time to decide which one of the two is the lesser evil and run with that as your choice.
Alderaan returns to the political hemisphere. This is interesting as you are interrogating a Thul nobleman who was caught up in a plot to kill several of the Organas; considering that this interrogation takes place in the Organa castle, you can imagine the sort of tact required of you. Indeed, going full-light side results in you freeing the nobleman's family and eventually securing his own freedom, which annoys an Organa who then in turn complains to General Garza who actually berates you for not being "diplomatic" enough. Oh, more details on the assignment of Alderaan? You're pursuing I think everyone's favourite Havoc member - as he is the first chap you meet of the team and he's rather cheerful - Gearbox. He, in turn, is pursuing something himself; the future of war. This future is a giant war droid which he then sets on you before finally facing death himself.
So, before taking on Harron Tavus, the only Squad members at this point who could potentially be alive are Jek Kardan, Wrait, and Fuse. All three of these figures could die if you pursue Dark options, so the light side "canon" is that Jek and Wraith are both alive. This means that Gearbox, Fuse, and Needles are all dead and Wraith, being Wraith, is considered incredibly unlikely to surrender should you see her again. If you spared her, you do indeed meet up with her on Tavus's ship, although this is one of the more interesting long-term effects in the game. Sparing Wraith and coming across her results in attempted subterfuge failing and the ship being made aware of your presence. Killing Wraith earlier, however, will result in you being able to continue your subtle subterfuge and potentially never being discovered or having to fight until you reach Tavus himself. It's a very interesting potential outcome. Incidentally, you also have the choice to kill or spare Tavus, but at the end of the day, half of the original squad died without any chances of saving them. Garza was right, you really do need to work on your diplomatic skills!
Chapter 2 begins with a rescue mission; you're saving a tech expert who, in hiding amongst Imperials, has discovered plans for a secret super-weapon, a special laser fitted to the front of a Star Destroyer which can fire at ships even when they're in Hyperspace. At this point your own squad consists of a medic, a robotic Scrappy-Doo, a cat, and yourself, and you need members who are more acquainted with explosions and technology in order to successfully destroy this thing. So Chapter 2 is all about completing your squad, and it doesn't disappoint.
Balmorra introduces you to a Weequay who has an annoying tendency to go off the record. Much like the Consular chapter 3, you are required to do something bizarre to show the Republic at its finest; in this case, recruiting a soldier who was formally dismissed from the Republic army. I will give credit, though, this does make more sense than finding an army which the Republic would never sanction in its right mind. He's gone crazy again and is trying his damnedest to locate a cache of weapons on Balmorra, doing such crazy antics as firing a missile straight at its supposed location. It makes sense somewhere. Hoth sees you join forces with a much more cooperative figure; a Gand, who is trying to recreate a unique wavelength and transmitter in order to help the war effort by creating the Star Wars equivalent of the Enigma machine. Whilst in the previous case on Balmorra you were forced to help out just to locate the damned guy, this time your recruit is immediately found and is working on something so important that you feel you should help him complete as he is the only one in the system with the technical know-how.
Once you complete your squad, you go and board the Gauntlet superweapon. This mission is perhaps one of the best-received of the entire game, and it's easy to see why. You get an amazing introductory cutscene - Republic navy bursting out of hyperspace with your BT-7 Thunderclap emerging in the centre - it's an awesome mission in general, and right at the beginning you get to fight alongside each and every single one of your companions! This sort of mission is annoyingly too rare; the only other time it happens is during the Bounty Hunter story, but you still lack a companion. Here, though, this is all five. It's a real shame that very few of the other classes see this, but it does make this class and this one mission all the more special for it.
The end of chapter 2 also sees us introduced to the figure who would become the chapter 3 boss: General Rakton, a loud and boistrous figure who declares war on the Republic for their act of unprovoked aggression on what he describes as a defense initiative. With one chapter still to go to see how this is dealt with, and with a promising second chapter, does the Trooper story live up to the build-up?
The answer, annoyingly, is no. Rather than focus more on the war with the Empire, you spend the vast majority of the third chapter recovering Republic assets so that they can be used against the Empire themselves. That said, this chapter actually begins with a rescue of Republic senators from Imperial soldiers. Whilst it's a shame that this does involve more politics, at least it presents the immediate threat of the Empire and Republic going to war and consequences thereof.
Belsavis sees you freeing an imprisoned team of starfighter pilots who bombed innocents in an attempt to kill a Sith Lord, who conveniently is on Belsavis himself. You free several of the crew, although the leader is already freed and chasing the Sith Lord, so you have to find both of them. Keeping in line with chapter 1, you either rescue him and let the Sith escape, or pursue and kill the Sith and let the squad leader die. Incidentally, saving the captain leads to facing one of the only Rancors you fight in a class story. In fact, I want to say that this is the only Rancor present in a class instance. So we had the conclusion to chapter 2 with all 5 companions present at once and now we have a Rancor fighting us. As strange as some of these missions are, this story does provide things which are unique and awesome.
There actually is another intervention which ties this back to war; you have to go to a prison complex and free many Republic prisoners. Whilst similar to Belsavis, at least this prison complex is actually Imperial! Indeed, it actually turns out to be a trap as Rakton proceeds to destroy it. This leads to an emotional choice behind freeing the Republic soldiers as planned or saving an Agent, by the name of Ava Jaxo, who provided help on Coruscant before catching up after Quesh. The choice between hundreds of soldiers and one specially-trained Agent is actually an incredibly heavy one, and is incredibly fitting in a chapter about war.
Voss re-unites you with the bomb which was given to the Separatists way back when on Ord Mantell. It also once more ties the intricacies of politics, but at least this time it is aware of how out-of-place it is in the context of the war. You're tasked with persuading a Republic senator that there is no military danger to Voss in order that he might give up his squadrons and allow them to move on to Corellia. None of these soldiers can believe that the senator is as stubborn as he is, and they're all desperate to be moved on to fight instead of being held on for no reason. Voss is the perfect planet for political stagnations of this nature, however, so the setting does make sense. Indeed, you even get a choice at the end to deliver the bomb to the Voss for diplomatic purposes - which the senator hates - or potentially upsetting the Voss and taking the bomb back to the Republic.
You move on to Corellia after stopping Rakton's attempts to nullify Havoc using a corrupt Republic Senator. In spite of the fact that all your character has done in this chapter has been to free Republic starfighter pilots and allow a senator's troops to leave Voss, Rakton is supposedly on the run and has been cornered. After helping the CorSec forces, you eventually discover a tank which you ride to Rakton's fortress and allow the Republic in. After a long-winded mission, you eventually defeat Rakton, and if you spare him you get given the choice on Coruscant by the Supreme Chancellor to turn him over for Republic prisoners-of-war or to keep him. Curiously, the choice to keep him is a Dark side option, even though it is by far the more sensible option of the two. This is also one of the reasons why I extremely dislike Leontyne Saresh, but that's another thing.
All in all, the Trooper has a good first chapter, a strong second chapter, and a weak third chapter. After the Smuggler and Consular stories, it's refreshing to have a story strong in both chapters 1 and 2, although it is a shame that chapter 3 falters. If it had kept the theme of war consistent throughout then perhaps it would have been more successful, although much like the Consular story it suffers from the available planets. In this case, a Republic-run prison planet and a planet whose name you could literally erase and replace with "political stagnation" do not make for good "Republic vs. Imperial" stories and do admittedly serve the more tailored stories which we received.
Regardless, the Trooper story does have some very good elements and has easily one of the best - if not the best - conclusions to the second chapter in the game as a whole.