Welcome to the boards!
No overlap in cards, nothing from one game is legal in the other. This really doesn't matter in the era of printability
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Important notes of comparison, off the top of my head:
- You still have personnel flying in ships to attempt missions.
- You still need to solve missions to win the game
- There's no seed phase. Your have a dilemma deck that behaves like the Q-Flash side deck in 1E - draw 1 dilemma per personnel attempting.
- There are no outposts, you have one or more HQ mission which is not attemptable and tells you what personnel you can play.
- Affilliations are less important. Your deck normally revolves around the people you can play at your HQ.
- All cards in your draw deck (except interrupts) have a cost, you get 7 counters to use per turn to pay for those costs
- Drawing happens when you pay one counter to draw one card
- You can't attempt your opponent's missions, but you can fly to them and disrupt their plans with infiltration or battle or assassination or assimilation or capture or ... the list goes on and on.
- Ship movement is different, the spaceline isn't linear, you fly directly from your current mission to the one you're going to. You just add the start and end span.
- Response timing is drastically simpler. Interrupts all respond to a specific thing "when you X" or "while Y is happening" and if they don't they're called orders.
- Orders are the actions you can take on your turn that aren't playing/drawing and it is very clear how you can't do one order during another.
- All the rules fit in one rulebook, total rules volume is way lower than even MtG.
- Lots of in-game optimisation decisions
Re treksense which is a common topic of comparison: the game lets you do pretty much everything that exists in Trek, with some gaps for gameplay over treksense. E.g. Voyager can fly from the DQ to Earth in one turn. Despite the non-treksense aspects of the rules, the way the cards actually work together in real games still brings a good sense of flavour. E.g. Voyager decks never include Earth.
See my signature about complexity: the game is still plenty complicated enough for Trek brains. There's just less gratuitous complexity about text in lore and gender and side decks and matching vs compatible and and and.