Right now plugins can only interact with peers, through the gateway. Besides, a single PeerConnection can at the moment be used by only one plugin, as that plugin is actually the "owner" of the PeerConnection itself. In next versions of Janus we'll work on stuff like plugins "chaining": that is, plugins that can act as "filters" for other plugins (e.g., transcoders) or as additional sources/sinks for the same PeerConnection of the same peer (e.g., to add recording functionality to a video conference using a different plugin).
Right now, we only support sessions with up to a single audio and/or a single video stream (as in, a single audio and/or video m-line) plus an optional DataChannel. Later versions of the gateway will add support for more media streams of the same type in a session.