Robin was blinded by floodlights and attacked by an unknown assailant. He threw two of his R darts low and turned to see what he'd hit: Batgirl. He checked the body, it was Lynx, not Cassie. Lynx had a broken neck and had been dead for at least three hours. The police arrived and saw Robin over her dead body. He escaped and got into his civilian clothes.
Oracle heard a police report on the Robin / Batgirl situation and sent the news to all who were listening.
In Africa, Nyssa al Ghul was killed when her car was bombed.
Tim visited with Alfred and Batman. He wanted to take the case himself since he was already involved. Batman agreed to let him take it. Cassie (?) watched the conversation from the shadows. On his way home, he realized it wasn't Batgirl's real outfit - his darts would have never pierced their kevlar. He suited up and headed to police HQ to investigate the body.

Robin got to the evidence room and found the costume. He found a partial finger print on the eye piece as he was spotted. He knocked the cop out, but his gun went off on his way down. Even with a full SWAT team alerted to his presence, Robin escaped by putting a police uniform on over his costume and simply walking out of the building.
Elsewhere, a woman was killed in an alleyway by someone calling her sister and preaching to her that she was a waste of talent.
Lady Shiva appeared in Robin's apartment with the news that Nyssa was killed. She believed the League of Assassins was at play. After she left, Robin found a coded message in the cowl of the fake Batgirl outfit:
We have Cassandra Cain bring David Cain to the Blaisdell oil fields at ten pm June seven or she dies tell no one or she dies.

Robin began his trek into Blackgate Prison by way of the sewer. He got to Cain's cell and knocked him out. When he woke up, he was tied (rather intricately) outside. Robin asked about Cassandra; he knew nothing. Robin knocked him out again.
One of Robin's snitches was approached by an unseen person. He was given a boomerang to deliver to the Boy Wonder.
When Robin landed his minicopter, he found they were surrounded by the League of Assassins. After Robin was beaten, Cassandra appeared. She was now in control of the League of Assassins. She confronted her father about the girl she'd killed - his other daughter, her own sister. Cassie offered Robin a partnership - the could deal out their own justice via the LoA. She gave him a gun and ordered him to kill Cain.

Robin refused to shoot; he and Cassandra struggled over the gun. She got control of it and shot her father. Before he died, he said Cassandra and her sister weren't the only one's he raised / trained.
A new "superhero" debuted in Gotham. He appeared to have the ability to teleport / disappear. Another man claimed he used to work for the Joker and a bomb would soon detonate and destroy the city.
Robin had to set some explosives to get free from the League, but Cassandra caught up to him. Their fight continued through a second explosion that blew them away from each other. Robin escaped not knowing whether Cassandra had survived or not. He found the League dead - their necks were broken. Cain's body was gone. He videotaped the whole thing, making him sure he could clear his name.
Back in the city, Robin's informant gave him the boomerang. He knew immediately it was from Captain Boomerang, Jr., the son of the man who'd killed his father.

Robin left a trail for Boomerang to find, but he never did. He changed clothes and met with his new tutor (due to family situations, he'd missed a lot of school). They both soon realized he didn't need a tutor, but he wanted to stay in good graces with his new school. Afterwards, he began moving into the Manor. He and Bruce talked about the adoption and Cassandra.
Robin met with officer Harper. She showed him the former Joker henchman, and his story about the bomb was feasible. At the location, he found what could be the bomb - his Geiger counter pinned out when he got close. He grabbed it and headed out. On the roof, Boomerang confronted him. Robin knocked him sideways and told him he didn't have time; Boomer insisted they team up on the bomb issue.

Boomer got Robin a list of probable supervillain hideouts from when he was in the Society. He took it through his snitch and Batman to knock some of the items off the list. After going through a couple, they bumped into a boy calling himself Dodge (the teleporter). He introduced himself as Robin's new sidekick. After a bit, they finally blew him off.
They visited old booby-trapped hideouts once belonging to Mad Hatter, Glassman, Dr. Double X, Dr. Phosphorous, Scarecrow, Cavalier, and Killer Croc. They finally hit paydirt at an old Ventriloquist place. They survived all the booby traps (including shooting Scarface robots) and got the bomb defused. Somewhere along the way, Robin realized he and Boomer made a good team.