"Fallout" begins five months after the events of the season five finale. Oliver, Diggle, and the rest of Team Arrow are in the process of stopping the missile that a bad guy has fired towards the city.
It cuts back to Lian Yu. Samantha wants to go back into the jungle to find William while the rest of the crew starts running off — explosions start going off.
Back at Arrow HQ in present day, Felicity brings food for the team to eat. Oliver and Felicity start talking about them — and Oliver's son William.
On the island, Oliver's talking to William — the former reassures the latter that he'll find Samantha.
Present day, Oliver has problems talking to William. He's busy playing video games and very standoffish. When Oliver wishes him goodnight, Williams refers to his dad as 'Oliver' instead of dad or father.
Dinah is interrogating the bad guy Team Arrow stopped at the beginning of the episode. A cop informs her that Lance is late to the station — he's at the bar.
At the police station, the criminal headbutts the table and reveals he has a C4 implant embedded in a tooth. He drops it into a can of soda, which explodes killing the officer we saw talking to Dinah earlier. Armed assailants storm the police station and they're led by Black Siren — she's busting the guy out.
Back at the police station, Lance reveals nine police officers were killed and six are critically wounded. Dinah shows security footage to Team Arrow that shows Black Siren leading the ambush. Diggle says he'll take the footage and show Lyla and ARGUS.
On Lian Yu, Oliver approaches Slade asking where Thea is. He says he knows and they start walking.
Present day, Lance approaches Oliver about the events on Lian Yu. He says that Black Siren was dead when they found her on the island after the blasts. Oliver gets a message that ARGUS has a lead on Black Siren.
Dinah stops the van Black Siren and her armored squad are traveling in. A fight busts out between the two groups.
During the fight, Wild Dog is shot and falls over the railing. Oliver leps over and catches him before crashing into a car below. Oliver's takes Wild Dog's helmet off and he's in bad shape.
Oliver reveals Wild Dog has a collapsed lung. The group discusses what steps to take next.
Oliver finds Thea on Lian Yu. She's unconscious.
Team Arrow is searching the place where Felicity last tracked Black Siren and her group. Dinah and Diggle talk about the incident on the bridge where Diggle missed shooting the mercenary that caused Wild Dog to fall over the edge.
On Lian Yu, Dinah and Lance are looking for Black Siren. The latter sneaks up behind them and holds knife to Dinah's throat before calling Lance "daddy."
Present day, Oliver goes to talk to William who's woken from a nightmare and he asks for the family's nanny. Williams say he sees the bad guy and when Oliver say he's confused, wondering who the bad guy is, Williams points at his father.
Lance tells Team Arrow that Black Siren wasn't dead when they found her on Lian Yu, rather he shot her to save Dinah.
On Lian Yu, Oliver finds Samantha who quickly dies in his arms.
Back in present-day Star City, Oliver and Lance are talking about fatherhood. Felicity walks in and tells the pair that they haven't found anything out of the ordinary. As she says that, Diggle sees a grenade roll in on the floor at Arrow HQ and as soon as it explodes, Black Siren and her posse walk in.
A fight breaks out with Diggle and Black Siren's henchmen, and with Diggle almost about to get shot, Oliver comes in to clean house.
The rest of Team Arrow comes in to fight and Black Siren and C4 guy manage to escape. In the alleyway outside, Lance runs into Black Siren and has her at gunpoint. She's able to talk her way out of it, using Laurel's likeness to persuade Lance not to shoot her.
Team Arrow decides to do
Oliver goes to see Rene in the hospital. The doctor wants to keep him a few extra days but he's getting ready to discharge himself. Oliver gives him an envelope with a letter — Oliver was able to get Rene another hearing in regards to the custody of his child.
Oliver leaves and enters another room at the hospital. It's Thea's room and she's in a coma. Slade walks in to tell Oliver that he's heading to Calgary to try and find his son.
Slade gives Oliver some fatherly advice and the two shake hands.
Diggle's getting dressed at Arrow HQ and it's revealed that he was injured rather badly in the blasts on Lian Yu. Dinah approaches him saying she's checked out his gun — he hasn't even been firing in, lying that he's been missing.
On Lian Yu,
Back at Oliver's house, he's talking to William about fatherhood — he tells William that the last thing William's mom said was that she wanted Oliver to take care of him. Oliver invites William to watch the game and William asks if it's football or baseball. After responding that it's a baseball game, William agrees and Oliver smiles.
Felicity calls and tells Oliver to turn on the TV. He does and a breaking news update reveals that a picture has captured the true identity of Green Arrow — his identity has been revealed.