The in game story was completely coherent. You wake up in Old Russia. You go to the tower, people refuse to tell you anything. You investigate fallen activity and end up making contact with Rasputin and the off world colonies. You go to the moon. You find that the hive are more active than anyone thought. You meet the stranger. You hamper the hive's rituals. The stranger tells you that something wicked this way comes. You go to Venus to investigate. You find out about the vex. The stranger tells you that the vex are a huge threat. You go to the reef. They tell you that you need a key to get into the black garden. You kill a gate lord. You get the key. You fight through the cabal, who occupy Mars. You open the gate to the black garden. You destroy its heart. You stop the actions that were draining the traveller of its light. This allows for the traveller to begin healing. If you did the archive side quest, you learn about the Vault Of Glass. You venture into the vault of glass and destroy Aetheon and thwart the vex's attempts at manipulating time. And of course everything you did were all baby steps as the true enemies haven't even arrived yet. Oryx being the first of many. I'm not going to say it was well put together or well presented. But it was there and it was coherent.