The second intifada (Sep 00-05) was a direct response to Israel breaking the terms of the Oslo Accords in two major ways. In the accords in 1993 Israel promised a stop to illegal settlement of the West Bank - instead Israel TRIPLED illegal settlements in the West Bank from 1993-2000.
The PLO recognised Israel as a state and affirmed its right to exist. In 1999, despite what it had agreed to in the Oslo accords, Israel refused to recognise a Palestinian state even though all the conditions for statehood had been fully met by the Palestinians (PLO).
Israel also renenged on the Oslo accords in 1994 by beginning construction of the West Bank separation wall and the bypass roads that no Palestinian was allowed to drive on. It wasn’t the building of a border wall itself so much as the decision to build it not along the agreed borders so that Palestinian land was being de facto annexed into Israel. Wherever the segments of the wall was being built, it included built in checkpoints. This was in addition to flying checkpoints.
After the second intifada started, it was then said the West Bank wall was built in response to it, but that is a bit of history revision as construction started in 1994 after the idea had been proposed in 1992 by PM Yitzhak Rabin who said that Israel must "take Gaza out of Tel Aviv"
In addition no Palestinian could drive back and forth from West Bank to Gaza or into Israel as many times as they wanted as from 1991 exit and entry permits were required.