Jason Todd in Arkham Asylum

Hey guys I just recently came across a video regarding Jason Todd's presence in Arkham Asylum. The video stated that Jason was actually escaping the Asylum during the events of Arkham Asylum. There are numerous videos ive seen that say this and it made me curious of something. We learn that for 2 years Joker had Jason in an abandoned wing of Arkham torturing him and im just wondering how this is possible ?

All these years I thought the Asylum was abandoned which is why Joker could keep him there like that. If he kept Jason in Arkham before/during the events of Asylum, how did he do it in a totally staffed and operational Arkham? Is there Lore i need to check out? Anyone have any insight?