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The purpose of this work is to present empirical data from a case study on the cognitive processes in the context of a web-based argumentation activity in a computer science course. Students used the iArgue web tool for argumentation and their interactions were structured by a collaboration script. The micro script supported argumentation and faded out while prompts reminded peers to check the validity of their partners' arguments after the fading of the micro script (peer-monitor). Our results demonstrate that combining fading out of the micro script and peer monitor could foster enhanced cognitive processing and improve the quality of single arguments and the quality of argumentation sequences in online asynchronous discussions.