The largest conflict in The Crucible relates to the difficult decision of whether or not to go along with the majority. John Proctor wavers in his decision for at least two reasons.
The first reason he wavers and considers signing a false confession is to save his life. If he confesses to witchcraft, Proctor will be allowed to live and raise his children. However, this means that he would be signing away his honor, as he sees it, and condemning the others who are awaiting hanging. Though they are already sentenced to die, there is doubt amongst the townspeople as to their actual guilt. If Proctor signs the confession, he will be removing that doubt.
Signing the confession also means that Proctor would be joining the majority, represented by Parris and Danforth, who urge him to confess and effectively corroborate the majority view that witchcraft has been taking place in Salem. The pressure of Parris and Danforth constitute Proctor's second reason for wavering in his decision.
We see in this two-part conflict the dual conflicts presented in the play. Proctor is faced with an internal conflict, regarding his own integrity and honor. He is also faced with an external conflict regarding whether or not to stand against the majority.
The final scene then offers a conclusion to both the internal and external conflicts faced by Proctor as he chooses honor and individuality in the end.