The ISDA Master Agreement has provisions common to all trades, such as the events that end the contract, how damages are determined on early termination, payment netting, collateral, and tax and legal treatment. In cases that went to court, a schedule was attached to the master agreement.
Consider a hypothetical example in which two financial institutions enter into two interest rate swaps and one cross-currency swap. The three trades sit under one master agreement, and a confirmation is exchanged for each trade.
The ISDA Master Agreement is one kind of master agreement, and master agreements are not limited to ISDA forms. Around 2013 in Japan, trades between financial institutions and ordinary corporations were handled with confirmations based on a bank transaction agreement.