Getting to Fatima
Being Catholic, visiting Fatima was one of the top reasons for this trip, hence we decided to start our trip with that visit. From my research I found out that getting by bus was the best option in terms of cost, time and options. There were primarily 2 bus companies: FlixBus and Rede Expressos. With Rede Expressos you have a few more time options because there are about 3 brands part of that network. However FlixBus had enough options for us and it seems slightly more convenient to book (they even take ApplePay). I found out Oriente station gave us the most direct route (nonstop). We booked our trip leaving around 11am and returning around 6pm. I figured 6 hours should be enough time for our visit (it ended up being about an hour short). Our roundtrip fare was about 60 EUR for a family of four (we booked about 2+ weeks ahead of time to get this fare).
We took an Uber to Oriente station. The buses depart from the parking right outside the Terminal. Our bus departed on time. I do recommend you pay the extra fee to book your seats ahead of time. The bus had wifi and worked surprisingly well. It also had USB ports but the one in our seats was not operational. Once you get to the Fatima bus station, the Basilica is within a 5 minute walk.
Shrine of Fatima
We started our visit to the Chapel of the Apparitions, the visited the Basilica of Our Lady of the Rosary of Fatima. To my surprise it was not too crowded, but it was a weekday and it wasn't a 13th of the month which I hear are the busiest days (May through October).
On your way from the Basilica of the Most Holy Trinity (new larger church) to the Basilica of the Our Lady of Fatima, on the right side there is a piece of the Berlin Wall that is easy to miss if you don't look for it.
Inside the Basilica of the Most Holy Trinity there are 3 additional chapels where you can attend mass if you have time. You can check the mass schedule here. There is also a museum that you cannot miss. That is where you can find the Crown of Our Lady of Fatima with one of the bullets with which Pope John Paul II was shot.
Where to eat
One of our Uber drivers had recommended Sao Francisco Churrasqueira, which is close to the house where Francisco and Jacinta lived, but since we were still in the Sanctuary area we decided to eat at Casa Platano, at that ended up being one of the best restaurants of our trip. Unless you are running short on time, I strongly recommend eating here, you won't be disappointed.
Pilgrimage to Lucia's house
As much as we would have liked to take the 130km pilgrimage from Lisbon to Fatima, we didn't have enough time in this trip. Instead we took a mini pilgrimage to Lucia's house via the Way of the Cross. From the Sanctuary walk 1km south on Dom Jose Alves Correia Avenue (same road you walked from the bus station) until you reach the roundabout with the Three Little Shepherds monument. From there search for the walking path with the "Via-Sacra/Caminho dos Pastorinhos" sign. That is a Way of the Cross with the 14 stations that will take you straight to Lucia's house.
After visiting Lucia's house, be sure to also visit Francisco and Jacinta's house which is just a couple blocks away. We decided to walk back to the Bus station via the way of the cross stopping at Loca do Cabeco (one of the apparition sites), and then through the 11-14th stations of the cross you can reach Calvario Hungaro.
Getting back to Lisbon
From Calvario Hungaro we took a nice trail path towards the Bus Station, but I would only advice taking this if you have GPS, as there were not a lot of trail signs in this path.
We had to rush back to the Bus Station only to find out that our bus was delayed 20 minutes. The FlixBus app showed this delay in the route details, but it did not notify me. I believe there was an option to opt in for notifications which I did not sign up for, so I suggest you opt in for this option. Other than that it was as smooth trip back to Lisbon Oriente and we took an Uber back to hour hotel.