First: In the comics Alex was a villain and worked with Pride betraying the rest of the group and was killed. So it looks like the series was sort of following this path because since the beginning they have been insinuating that he wanted the powers of the others. Then in the Cloak and Dagger episode Tandy saw that his greatest hope was to have taken those powers from the others. So evil Alex isn't really coming out of nowhere.
The past 2016. This is the time just before the Runaways first got back together. In other words the start of the series.
Current time 2019. The Runaways just fought Morgana and Gert died.
Future 2022. After Gert dies we jump a couple years forward. Nico took off to study mystic stuff. Karolina has a new girlfriend named Julie. Molly is back in school as a Senior about to graduate. Chase has become a recluse locked in his lab working on time travel. Alex has taken after his parents and is running a mega company with his dad.
Further future 2028 Chase has solved the problem of time travel and plans to go back to 2019 and save Gert. Alex has gone full villain and the rest of the Runaways have turned against him. Somebody, possibly one of the Runaways has made an attempt on Alex's life with a bomb. Because Alex helped solve the time travel equations he also has access to time travel. Alex decides to go back to 2022 and kill the others so they never get a chance to turn against him. Chase puts aside his saving Gert plan till he can stop Alex so he follows him back to 2022.
OK, so now we have Chase and Alex from 2028 running around in timeline 2022. Alex's attempts to kill the others fails because Chase has warned them and because Nico is more powerful than Alex knew. So he flees to 2016 to stop them before they ever became a group. Chase recruits the 2022 runaways (except for the 2022 Chase who is still in his lab) And they jump back to stop Alex. They all go back and interact with themselves a bit and then manage to stop 2028 Alex. 2028 Alex says he will go along with their plan to save Gert.
The 2022 crew plus 2028 Alex and Chase go to 2019 so at this point we have the parents, 2019 Gert, 2019 Chase, 2028 Chase, 2019 Alex, 2022 Alex, 2028 Alex, 2019 Molly, 2022 Molly, 2019 Nico, 2022 Nico, 2019 Karolina, 2022 Karolina.
So the things that get altered in 2019 are that they save Gert but 2022 Chase gets killed. 2022 Nico tells 2019 Nico not to run away from Karolina but to stay and face the future together. But then she wipes her mind to forget how she got that idea. And lastly 2028 Alex left 2019 Alex a note telling him to kill Nico. Then all the 2022 and 2028 people fade away because the timeline has been altered due to saving Gert.
So if there were a season 4 then Alex probably would have been the big bad.