Assuming your runners are not Epic(*) powerful, they cannot piss off one of the AAA company enough that they will hunt them down to the ends of the world. Well, they could but it takes effort and skill they do not have. In the same way as myself would find it incredibly difficult to piss off the European Union. It is possible but would be hard. Even, if you did, you can still escape -- see Snowden and the NSA abuse.
(*) By Epic I mean can go toe-to-toe with dragons, Horrors, and have the resources to mess with most nation states. Most often than not, these are not really normal cyberpunk games.
Companies, and governments, and any large organisation is made up of competing individual. All will do their best of cover their tracks and do their best to get blackmail material on others. This is the cyberpunk way. This is where your runners come in: they as deniable black ops for one executive to get dirty on another. Your runners are never against Ares, but are against Bob while having the support of Alice. If the run succeeds, Bob can be pissed but their direct boss Fred might just sack Bob since he's clearly incompetent and put Alice in charge of finding the leak: which she can fake really easily.
If not, someone from an external company can provide shelter just like the freedom loving Russia (wait, what⸮) provided to Snowden. If the leak is big enough, the runners might just use that as blackmail: leave us alone or we'll tell the world about your clown porn fetish!
Your job as a GM is to make sure all those subtle connections and interactions are there.
Gangs, organise crime, corrupt cops, corrupt politicians, ecological disasters, ... Just read some local news and you'll get a hundred ideas for plots. If you don't want to be too depressed, look at your favourite TV show and ripe the plots out of that: Breaking Bad, The Wire, Bracco, Spiral, ... Hundreds of run ideas right there.
Get your players involved in the design of the game...
No, seriously. Get the players to write the plots for you. Ask them what they would like to do, to explore around their characters. Do they want to rise up as tragic heroes fighting for freedom? Do they want to get money, no matter the cost? Do they want to see deep down the rabbit hole they can travel while retaining their humanity? Do they want to explore racism, cults, and alternate religions?
Involve the players and your plots will become so much better.