My predictions:
1) Enclave releases FEV in the vaults. Good chunk of the residents mutate, some escape. Enclave shows up and Norm, Stephanie, and maybe some others get taken to Colorado (Claudia, Chet, etc). Norm and Stephanie act as our POV at Enclave
2) House proposes a mutual deal with Lucy/Max to counter Legion. NCR is wary but outnumbered they agree. House tempts Lucy with Enclave knowledge, Max is skeptical because Cooper told Max he was going to give cold fusion to someone bad
3) Liberty Prime Alpha gets built and ends the civil war. Quintus realizes Commonwealth has their own Liberty prime and therefore they need a leg up. BoS spy reports cold fusion might be in Vegas, which would make their prime more powerful. BoS attacks and House takes control of prime using Robco back door access, forcing BoS to retreat or surrender
4) Coop meets more ghouls/mutants on way to Colorado
5) Coop finally gets to Colorado. Mutants/ghouls with him get defeated. One Enclave is revealed to be Laney Howard, now an indoctrinated Enclave officer (my guess is she was de thawed about 10-15 years prior). She has Coop taken into custody for experimentation. Betty is being controlled by a mind device as punishment .
6) House Liberty prime and others attack the Enclave facility. Prime gets fatally damaged, House consciousness escapes somehow if he fully transferred to it. Coop finally gets through to his daughter, but he dies. His family escape the facility along with other vault survivors. Final scene teases the Institute