In the following issue, the district attorney decided to charge the Flash with manslaughter. In the next issue, the Flash was arrested.
In Flash #327, the grand jury decided to indict the Flash. Meanwhile, his Justice League teammates decide on whether he will be kicked out of the League due to him killing the Reverse Flash. The League is shockingly kind of half-assed about it. They don't even have the whole roster come in to vote on the topic. In the end, Superman is the deciding vote. The issue ends with a cliffhanger. Then, in one of the boldiest (or perhaps irritating?) moves imaginable, the next issue opens with Superman about to make his decision and then the rest of the issue if a reprint of a classic Silver Age Flash/Reverse Flash issue, with the issue ending with a second cliffhanger that was the same cliffhanger as the previous issue! Yes, Superman seriously ended one issue with "This is my decision" and then the next issue also ended with "This is my decision."
In Flash #329, Superman votes against automatic expulsion, but if the Flash is found guilty, he still gets kicked off of the team. Flash, rightly so, tells the team, "Yeah, sure, I can't exactly be worried about this right now." The Flash hires an old friend of Barry Allen, Peter Farley, as his lawyer. Meanwhile, we see that Fiona has seriously snapped from the effects of Barry's disappearance and is now in a mental institution, where Barry's parents visit her and she is not doing well. Meanwhile, he has had to ditch his Barry Allen identity all together while all of this is going on.
The next couple of issues were mostly unrelated to the trial, but then in Flash #332, someone tries to kill the Flash's lawyer. The Flash saves him from dying, but he is still badly injured.
Peter's partner agrees to take on the case with her partner out of commission, but she lets Flash know that she is doing it begrudgingly in Flash #333 (meanwhile, the underhanded defense attorney, N.D. Redik, wants the case badly, but Flash won't accept him).
Cecile Horton also almost died in an explosion by some goons hired by Redik to eliminate the competition (the dead woman is not Horton).
Through all of this, the Rogues have been using all of their powers to turn Central City's views against the Flash. So public sentiment is not in the Flash's favor at the moment. After defeating the Pied Piper, the Piper also suffers a nervous breakdown and the Rogues blame the Flash. They create a super-powerful new villain called Big Sir to punish the Flash. The Flash manages to convince Big Sir to not attack him. This brings us to Flash #340, now 17 issues into the storyline and the trial has finally begun! Oh, by the way, the charges were re-filed and now the Flash was on trial for second-degree murder!
The Rogues, though, brainwash Big Sir and force him to attack the Flash again (yes, we are spending an awful lot of time on Big Sir) and Big Sir beats the Flash nearly to death, leaving him barely recognizable as Barry Allen anymore.
King Solovar uses the technology of Gorilla City to heal Barry's injuries. Around the same time, Barry learns why his lawyer hates him. She was convinced by a supervillain, Goldface, that the Flash had called Goldface's bluff on an ultimatum and her father was killed when Goldface carried through on his threat. She ultimately learns that Goldface lied about the whole thing and she reconciles with the Flash.
In the next issue, Wally West, Kid Flash, is subpoenaed to testify against the Flash. Most of this issue was also reprints of old Flash/Kid Flash stories, but it ends with Wally testifying that it was not necessary for Flash to kill the Reverse Flash!
Things were not looking good for the Scarlet Speedster...