Blockchain remains, but it's will only contain hash of transaction script. Actual transaction script body which is heavy and take most of space in blockchain will go into separate extended block. This reduces size of transactions in main chain.
You might want to check this 5 minute segregated witness explained video:
https://youtu.be/OFfBRzh9HmU
Or this 50 minute presentation from actual Bitcoin developer and initiator of segwit:
https://youtu.be/NOYNZB5BCHM