It'd be interesting if Lev and Abby joined the Fireflies. Since the Fireflies know Abby's dad and chapter were working on a cure in Salt Lake, Abby could play a role in recovering data files, equipment, and talent in order to progress a cure. This can be more interesting in a couple ways: Abby knows a cure requires someone with immunity, like Ellie, but she is hesitant to seek her out or reveal to the Fireflies that she exists due to the pair's complicated history. For plot sake, lets say she keeps this information hidden, but her and Lev are able to help progress the cure by creating a vaccine that slows the rate of infection.
Here's where it gets interesting: Lev gets bit on an equipment supply run and the Fireflies inject him to slow the infection. Abby and co. are dismayed, as they know it's just a matter of time until he turns. So, out of desperation, Abby reveals the existence of Ellie and takes it upon herself to find her in order to produce a cure.
Now, picking up Ellie's story after Part II, who has forgiven Joel and understood Abby (but not fully forgiven), we find her back in Jackson as somewhat of a social outcast. Tommy is upset that she didn't commit to revenge against Abby once he inquires about the outcome of her trip to Santa Barbra. Maria is upset that Ellie let revenge consume herself and Tommy. And Dina still has love for Ellie, but she cannot forgive her for abandoning her and JJ. Ellie quickly comes to realize that while she has come to peace with a lot of things, there is no place for her in Jackson. Who wants to be the pariah of a small, isolated community? So Ellie wants to reclaim her image and become a beacon of hope for desperate people. She wants to make her life mean something instead of living the passive existence gifted to her by Joel. So she sets out to explore the country and try to do some good.
Picking back up with Abby, she arrives at Jackson and scopes out the place trying to see if Ellie is there. She enters the community in disguise and finds out that Ellie is no longer there. While she is there Tommy recognizes her and she flees Jackson in a hurry.
Picking back up with Ellie, she keeps running into communities but finds herself still an outcast. No one accepting her, having no purpose. She just continues looking for a hint of where she can fit in. Essentially, she travels all up and down the West Coast but no luck.
Pan back to Abby, she is being hunted by Tommy and some friends while picking up Ellie's scant trail. After a bit of being hunted she finds Ellie in Boston, visiting the mall in which Riley and her were bitten. She turns around and she see Abby, and she is filled with a mix of anger and embarrassment. She lashes out and demands to know why she is here. Then Abby makes her case: She tells Ellie that she wanted to avoid her, but she needs her help. She talks about Lev's situation, but she is still unwilling to help. Abby then mentions that Ellie's sacrifice could save humanity. Ellie doesn't answer, but then they are attacked by a bunch of infected and Abby saves her life. Ellie then agrees to back to the Fireflies and finish what she and Joel had started in Part 1. She still holds animosity for Abby but agrees to travel back with her because she wants meaning and recognizes this is the opportunity she was looking for.
Making their way across the country, the pair grow beyond understanding and to some degree forgive one another. They still aren't best of friends; it's a cold relationship. Eventually, Tommy catches up with the pair and takes his revenge on Abby. Ellie is a bit distraught and doesn't know what to do. She curses Tommy and decides to complete the mission to save Lev herself, fully forgiving Abby and realizing that this cycle of violence has to stop.
In the end, Ellie meets up with the Fireflies and she gives her life to make a cure. Returning meaning to her life and making it all mean something.
That's what I came up with really quick.